;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix build-system python)
#:use-module (guix build-system r)
#:use-module (guix build-system ruby)
+ #:use-module (guix build-system scons)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
+ #:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages cran)
#:use-module (gnu packages parallel)
#:use-module (gnu packages pdf)
#:use-module (gnu packages perl)
+ #:use-module (gnu packages perl-check)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-web)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
(define-public bedtools
(package
(name "bedtools")
- (version "2.26.0")
+ (version "2.27.1")
(source (origin
(method url-fetch)
- (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
+ "download/v" version "/"
+ "bedtools-" version ".tar.gz"))
(sha256
(base32
- "0xvri5hnp2iim1cx6mcd5d9f102p5ql41x69rd6106x1c17pinqm"))))
+ "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
(build-system gnu-build-system)
- (native-inputs `(("python" ,python-2)))
- (inputs `(("samtools" ,samtools)
- ("zlib" ,zlib)))
(arguments
'(#:test-target "test"
+ #:make-flags
+ (list (string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
- (delete 'configure)
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (for-each (lambda (file)
- (install-file file bin))
- (find-files "bin" ".*")))
- #t)))))
+ (delete 'configure))))
+ (native-inputs `(("python" ,python-2)))
+ (inputs
+ `(("samtools" ,samtools)
+ ("zlib" ,zlib)))
(home-page "https://github.com/arq5x/bedtools2")
(synopsis "Tools for genome analysis and arithmetic")
(description
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))))
+ "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))
+ (arguments
+ '(#:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*")))
+ #t)))))))
(define-public ribotaper
(package
"-2017-0621-source.tar.gz"))
(sha256
(base32
- "1386dg2npx8p62wmv08mjzsd2z3waknb9j1gg3gkvblcy57hymnn"))))
+ "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
(define-public cutadapt
(package
(name "cutadapt")
- (version "1.12")
+ (version "1.14")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "19smhh6444ikn4jlmyhvffw4m5aw7yg07rqsk7arg8dkwyga1i4v"))))
+ "16gbpiwy4m48vq2h5wqar3i8vr6vcj9gcl2qvqim19x6ya9dp8kd"))))
(build-system python-build-system)
(arguments
`(#:phases
(define-public diamond
(package
(name "diamond")
- (version "0.9.12")
+ (version "0.9.14")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1zrnr59pqdg56wxfdx3xg4h4d8fa14cxq5kfmc3q88hxrj42rqgs"))))
+ "07li3chjdna0wjyh680j3bhwiqh1fbfq9dy9jxxs82mc0rw0m1yy"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
(method url-fetch)
(uri (string-append
"http://eddylab.org/software/hmmer"
- (version-prefix version 1) "/"
+ (version-major version) "/"
version "/hmmer-" version ".tar.gz"))
(sha256
(base32
(define-public java-htsjdk
(package
(name "java-htsjdk")
- (version "1.129")
+ (version "2.3.0") ; last version without build dependency on gradle
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
+ "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq"))
(modules '((guix build utils)))
- ;; remove build dependency on git
- (snippet '(substitute* "build.xml"
- (("failifexecutionfails=\"true\"")
- "failifexecutionfails=\"false\"")))))
+ (snippet
+ ;; Delete pre-built binaries
+ '(begin
+ (delete-file-recursively "lib")
+ (mkdir-p "lib")
+ #t))))
(build-system ant-build-system)
(arguments
`(#:tests? #f ; test require Internet access
+ #:jdk ,icedtea-8
#:make-flags
(list (string-append "-Ddist=" (assoc-ref %outputs "out")
"/share/java/htsjdk/"))
(modify-phases %standard-phases
;; The build phase also installs the jars
(delete 'install))))
+ (inputs
+ `(("java-ngs" ,java-ngs)
+ ("java-snappy-1" ,java-snappy-1)
+ ("java-commons-compress" ,java-commons-compress)
+ ("java-commons-logging-minimal" ,java-commons-logging-minimal)
+ ("java-commons-jexl-2" ,java-commons-jexl-2)
+ ("java-xz" ,java-xz)))
+ (native-inputs
+ `(("java-testng" ,java-testng)))
(home-page "http://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description
manipulating HTS data.")
(license license:expat)))
+;; This version matches java-htsjdk 2.3.0. Later versions also require a more
+;; recent version of java-htsjdk, which depends on gradle.
+(define-public java-picard
+ (package
+ (name "java-picard")
+ (version "2.3.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/broadinstitute/picard.git")
+ (commit version)))
+ (file-name (string-append "java-picard-" version "-checkout"))
+ (sha256
+ (base32
+ "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete pre-built binaries.
+ (delete-file-recursively "lib")
+ (mkdir-p "lib")
+ (substitute* "build.xml"
+ ;; Remove build-time dependency on git.
+ (("failifexecutionfails=\"true\"")
+ "failifexecutionfails=\"false\"")
+ ;; Use our htsjdk.
+ (("depends=\"compile-htsjdk, ")
+ "depends=\"")
+ (("depends=\"compile-htsjdk-tests, ")
+ "depends=\"")
+ ;; Build picard-lib.jar before building picard.jar
+ (("name=\"picard-jar\" depends=\"" line)
+ (string-append line "picard-lib-jar, ")))
+ #t))))
+ (build-system ant-build-system)
+ (arguments
+ `(#:build-target "picard-jar"
+ #:test-target "test"
+ ;; Tests require jacoco:coverage.
+ #:tests? #f
+ #:make-flags
+ (list (string-append "-Dhtsjdk_lib_dir="
+ (assoc-ref %build-inputs "java-htsjdk")
+ "/share/java/htsjdk/")
+ "-Dhtsjdk-classes=dist/tmp"
+ (string-append "-Dhtsjdk-version="
+ ,(package-version java-htsjdk)))
+ #:jdk ,icedtea-8
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-our-htsjdk
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "build.xml"
+ (("\\$\\{htsjdk\\}/lib")
+ (string-append (assoc-ref inputs "java-htsjdk")
+ "/share/java/htsjdk/")))
+ #t))
+ (add-after 'unpack 'make-test-target-independent
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "build.xml"
+ (("name=\"test\" depends=\"compile, ")
+ "name=\"test\" depends=\""))
+ #t))
+ (replace 'install (install-jars "dist")))))
+ (inputs
+ `(("java-htsjdk" ,java-htsjdk)
+ ("java-guava" ,java-guava)))
+ (native-inputs
+ `(("java-testng" ,java-testng)))
+ (home-page "http://broadinstitute.github.io/picard/")
+ (synopsis "Tools for manipulating high-throughput sequencing data and formats")
+ (description "Picard is a set of Java command line tools for manipulating
+high-throughput sequencing (HTS) data and formats. Picard is implemented
+using the HTSJDK Java library to support accessing file formats that are
+commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
+VCF.")
+ (license license:expat)))
+
+;; This is the last version of Picard to provide net.sf.samtools
+(define-public java-picard-1.113
+ (package (inherit java-picard)
+ (name "java-picard")
+ (version "1.113")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/broadinstitute/picard.git")
+ (commit version)))
+ (file-name (string-append "java-picard-" version "-checkout"))
+ (sha256
+ (base32
+ "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete pre-built binaries.
+ (delete-file-recursively "lib")
+ (mkdir-p "lib")
+ #t))))
+ (build-system ant-build-system)
+ (arguments
+ `(#:build-target "picard-jar"
+ #:test-target "test"
+ ;; FIXME: the class path at test time is wrong.
+ ;; [testng] Error: A JNI error has occurred, please check your installation and try again
+ ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
+ #:tests? #f
+ #:jdk ,icedtea-8
+ ;; This is only used for tests.
+ #:make-flags
+ (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
+ #:phases
+ (modify-phases %standard-phases
+ ;; Do not use bundled ant bzip2.
+ (add-after 'unpack 'use-ant-bzip
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "build.xml"
+ (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar")
+ (string-append (assoc-ref inputs "ant")
+ "/lib/ant.jar")))
+ #t))
+ (add-after 'unpack 'make-test-target-independent
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "build.xml"
+ (("name=\"test\" depends=\"compile, ")
+ "name=\"test\" depends=\"compile-tests, ")
+ (("name=\"compile\" depends=\"compile-src, compile-tests\"")
+ "name=\"compile\" depends=\"compile-src\""))
+ #t))
+ (add-after 'unpack 'fix-deflater-path
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "src/java/net/sf/samtools/Defaults.java"
+ (("getStringProperty\\(\"intel_deflater_so_path\", null\\)")
+ (string-append "getStringProperty(\"intel_deflater_so_path\", \""
+ (assoc-ref outputs "out")
+ "/lib/jni/libIntelDeflater.so"
+ "\")")))
+ #t))
+ ;; Build the deflater library, because we've previously deleted the
+ ;; pre-built one. This can only be built with access to the JDK
+ ;; sources.
+ (add-after 'build 'build-jni
+ (lambda* (#:key inputs #:allow-other-keys)
+ (mkdir-p "lib/jni")
+ (mkdir-p "jdk-src")
+ (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
+ "-xf" (assoc-ref inputs "jdk-src")))
+ (zero? (system* "javah" "-jni"
+ "-classpath" "classes"
+ "-d" "lib/"
+ "net.sf.samtools.util.zip.IntelDeflater"))
+ (with-directory-excursion "src/c/inteldeflater"
+ (zero? (system* "gcc" "-I../../../lib" "-I."
+ (string-append "-I" (assoc-ref inputs "jdk")
+ "/include/linux")
+ "-I../../../jdk-src/src/share/native/common/"
+ "-I../../../jdk-src/src/solaris/native/common/"
+ "-c" "-O3" "-fPIC" "IntelDeflater.c"))
+ (zero? (system* "gcc" "-shared"
+ "-o" "../../../lib/jni/libIntelDeflater.so"
+ "IntelDeflater.o" "-lz" "-lstdc++"))))))
+ ;; We can only build everything else after building the JNI library.
+ (add-after 'build-jni 'build-rest
+ (lambda* (#:key make-flags #:allow-other-keys)
+ (zero? (apply system* `("ant" "all" ,@make-flags)))))
+ (add-before 'build 'set-JAVA6_HOME
+ (lambda _
+ (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
+ #t))
+ (replace 'install (install-jars "dist"))
+ (add-after 'install 'install-jni-lib
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((jni (string-append (assoc-ref outputs "out")
+ "/lib/jni")))
+ (mkdir-p jni)
+ (install-file "lib/jni/libIntelDeflater.so" jni)
+ #t))))))
+ (inputs
+ `(("java-snappy-1" ,java-snappy-1)
+ ("java-commons-jexl-2" ,java-commons-jexl-2)
+ ("java-cofoja" ,java-cofoja)
+ ("ant" ,ant) ; for bzip2 support at runtime
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("ant-apache-bcel" ,ant-apache-bcel)
+ ("ant-junit" ,ant-junit)
+ ("java-testng" ,java-testng)
+ ("java-commons-bcel" ,java-commons-bcel)
+ ("java-jcommander" ,java-jcommander)
+ ("jdk" ,icedtea-8 "jdk")
+ ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop")))))))
+
(define-public htslib
(package
(name "htslib")
(define-public idr
(package
(name "idr")
- (version "2.0.0")
+ (version "2.0.3")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
+ "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3"))
+ ;; Delete generated C code.
+ (snippet
+ '(begin (delete-file "idr/inv_cdf.c") #t))))
(build-system python-build-system)
- (arguments
- `(#:tests? #f)) ; FIXME: "ImportError: No module named 'utility'"
+ ;; There is only one test ("test_inv_cdf.py") and it tests features that
+ ;; are no longer part of this package. It also asserts False, which
+ ;; causes the tests to always fail.
+ (arguments `(#:tests? #f))
(propagated-inputs
`(("python-scipy" ,python-scipy)
("python-sympy" ,python-sympy)
"The IDR (Irreproducible Discovery Rate) framework is a unified approach
to measure the reproducibility of findings identified from replicate
experiments and provide highly stable thresholds based on reproducibility.")
- (license license:gpl3+)))
+ (license license:gpl2+)))
(define-public jellyfish
(package
(name "jellyfish")
- (version "2.2.4")
+ (version "2.2.7")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/gmarcais/Jellyfish/"
"/jellyfish-" version ".tar.gz"))
(sha256
(base32
- "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk"))))
+ "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q"))))
(build-system gnu-build-system)
(outputs '("out" ;for library
"ruby" ;for Ruby bindings
`(("bc" ,bc)
("time" ,time)
("ruby" ,ruby)
- ("python" ,python-2)))
+ ("python" ,python-2)
+ ("pkg-config" ,pkg-config)))
+ (inputs
+ `(("htslib" ,htslib)))
(synopsis "Tool for fast counting of k-mers in DNA")
(description
"Jellyfish is a tool for fast, memory-efficient counting of k-mers in
(base32
"1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
(patches (search-patches "metabat-fix-compilation.patch"))))
- (build-system gnu-build-system)
+ (build-system scons-build-system)
(arguments
- `(#:phases
+ `(#:scons ,scons-python2
+ #:scons-flags
+ (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost")))
+ #:tests? #f ;; Tests are run during the build phase.
+ #:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-includes
(lambda _
"/lib'"))
;; Do not distribute README.
(("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
- #t))
- (delete 'configure)
- (replace 'build
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (mkdir (assoc-ref outputs "out"))
- (zero? (system* "scons"
- (string-append
- "PREFIX="
- (assoc-ref outputs "out"))
- (string-append
- "BOOST_ROOT="
- (assoc-ref inputs "boost"))
- "install"))))
- ;; Check and install are carried out during build phase.
- (delete 'check)
- (delete 'install))))
+ #t)))))
(inputs
`(("zlib" ,zlib)
("perl" ,perl)
("samtools" ,samtools)
("htslib" ,htslib)
("boost" ,boost)))
- (native-inputs
- `(("scons" ,scons)))
(home-page "https://bitbucket.org/berkeleylab/metabat")
(synopsis
"Reconstruction of single genomes from complex microbial communities")
(version "0.5.4")
(source (origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/m/misopy/misopy-"
- version ".tar.gz"))
+ (uri (pypi-uri "misopy" version))
(sha256
(base32
"1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip"))
(define-public roary
(package
(name "roary")
- (version "3.8.2")
+ (version "3.11.0")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "03dfr2cd5fp80bcr65923zpdzrasvcxl7c2vgh8373v25a1yfap7"))))
+ "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i"))))
(build-system perl-build-system)
(arguments
`(#:phases
(inputs
`(("perl-array-utils" ,perl-array-utils)
("bioperl" ,bioperl-minimal)
+ ("perl-digest-md5-file" ,perl-digest-md5-file)
("perl-exception-class" ,perl-exception-class)
("perl-file-find-rule" ,perl-file-find-rule)
("perl-file-grep" ,perl-file-grep)
(define-public subread
(package
(name "subread")
- (version "1.5.1")
+ (version "1.6.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/subread/subread-"
version "/subread-" version "-source.tar.gz"))
(sha256
(base32
- "0gn5zhbvllks0mmdg3qlmsbg91p2mpdc2wixwfqpi85yzfrh8hcy"))))
+ "0ah0n4jx6ksk2m2j7xk385x2qzmk1y4rfc6a4mfrdqrlq721w99i"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no "check" target
(define-public r-vegan
(package
(name "r-vegan")
- (version "2.4-4")
+ (version "2.4-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "vegan" version))
(sha256
(base32
- "1n57dzv2aid6iqd9fkqik401sidqanhzsawyak94qbiyh6dbd1x9"))))
+ "0cyyvn3xsjn24w590jn6z4xajafv7yzvj6c51vqi9q6m8v5831ya"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.56.0")
+ (version "1.56.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "0wlrp3v2jxw9is98ap39dfi7z97kmw1wv1xi4h7yfh12zpj2r8l0"))))
+ "14c5xd9kasvcwg5gbjys2c1vizxhlqlzxakqc2kml0kw97hmx0rq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
microarrays.")
(license license:artistic2.0)))
+(define-public r-copynumber
+ (package
+ (name "r-copynumber")
+ (version "1.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "copynumber" version))
+ (sha256
+ (base32
+ "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-s4vectors" ,r-s4vectors)
+ ("r-iranges" ,r-iranges)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-biocgenerics" ,r-biocgenerics)))
+ (home-page "https://bioconductor.org/packages/copynumber")
+ (synopsis "Segmentation of single- and multi-track copy number data")
+ (description
+ "This package segments single- and multi-track copy number data by a
+penalized least squares regression method.")
+ (license license:artistic2.0)))
+
(define-public r-geneplotter
(package
(name "r-geneplotter")
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "1hcxnkkjfvz4hj8iqidshwsjq7jnl1z7wj63dvcwlx1zx5aichyh"))))
+ "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(propagated-inputs
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.24.0")
+ (version "1.24.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "0qxwnz2ffhav9slcn095k206cfza9i3i5l7w1154plf08gpy1d1d"))))
+ "18nh8ynxirfwkmc4sawdxgl7w1sl9ny5zpv8zbhv9vi5vgb8pxmj"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gseabase
(package
(name "r-gseabase")
- (version "1.40.0")
+ (version "1.40.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "0kpkl6c5lrar6ip7wlhvd5axqlb9lb5l3lgbdb3dlih32c3nz0yq"))))
+ "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz"))))
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
(define-public vsearch
(package
(name "vsearch")
- (version "2.5.2")
+ (version "2.6.0")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1z10psrwhflchwzw1fvzwnsn59xglf94qrn7msj93fpnjgafvmks"))
+ "0rplgpvsdkxw0k371ckxrp6i77jn93ckhslaazwbyd85m83nkynr"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.6.0")
+ (version "2.6.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "05f2j9fx8s5gh4f8qkl6wcz32ghz04wxhqb3xxcn1bj24qd7x1x8"))))
+ "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
(define-public r-getopt
(package
(name "r-getopt")
- (version "1.20.0")
+ (version "1.20.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "getopt" version))
(sha256
(base32
- "00f57vgnzmg7cz80rjmjz1556xqcmx8nhrlbbhaq4w7gl2ibl87r"))))
+ "0m463mcvixh54i3ng42n0vxmdlf97dgbfs2sf9wnjm782ddw68hm"))))
(build-system r-build-system)
(home-page "https://github.com/trevorld/getopt")
(synopsis "Command-line option processor for R")
(define-public r-genomeinfodbdata
(package
(name "r-genomeinfodbdata")
- (version "0.99.0")
+ (version "0.99.1")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
version ".tar.gz"))
(sha256
(base32
- "120qvhb0pvkzd65lsgja62vyrgc37si6fh68q4cg4w5x9f04jw25"))))
+ "0hipipvyvrh75n68hsjg35sxbcfzrghzxv547vnkk2f8ya99g01r"))))
(properties
`((upstream-name . "GenomeInfoDbData")))
(build-system r-build-system)
(define-public r-edger
(package
(name "r-edger")
- (version "3.20.1")
+ (version "3.20.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "01qnxwr9rmz8r5ga3hvjk632365ga2aygx71mxkk7jiad2pjznsp"))))
+ "0j5s3i33qmld9l7gs1rzpv601zxyqz711x8mq35hml088c8s99w9"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.24.0")
+ (version "1.24.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "1lllp2vgyfbrar1yg28ji7am470hfzrzxm1bgdk68xpnrwcgcl25"))))
+ "19wgb2kcqy97pm3xgqc781id9fbmzp1hdwzkkhdzpvyf29w4n29j"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
(define-public r-limma
(package
(name "r-limma")
- (version "3.34.0")
+ (version "3.34.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "0a15gsaky0hfrkx8wrrmp0labzxpq6m2hrd33zl206wyas8bqzcs"))))
+ "1vcxf9jg8xngxg5kb9bp8rw5sghpnkpj320iq309m2fp41ahsk3f"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.32.1")
+ (version "2.34.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "0fhpbjlsgbqxrpj6nzhhk9q3ph81n5x4p7mmd097xjjn6b05w1d8"))))
+ "0jzv8b86vpvavwnzi5xf7y18xmn72zkabkn2kclg1mgl847cq13k"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
+ ("r-httr" ,r-httr)
+ ("r-progress" ,r-progress)
("r-rcurl" ,r-rcurl)
+ ("r-stringr" ,r-stringr)
("r-xml" ,r-xml)))
(home-page "https://bioconductor.org/packages/biomaRt")
(synopsis "Interface to BioMart databases")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.10.1")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "08mdfxyk9nwz77v0xhlvs19p2wj0phgm5c5b25vm0xh3749njsp0"))))
+ "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
(propagated-inputs
`(("r-futile-logger" ,r-futile-logger)
- ("r-snow" ,r-snow)))
+ ("r-snow" ,r-snow)
+ ("r-bh" ,r-bh)))
(home-page "https://bioconductor.org/packages/BiocParallel")
(synopsis "Bioconductor facilities for parallel evaluation")
(description
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.14.0")
+ (version "1.14.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "0sw30lj11wv7ifzypqm04lcah987crqwvj48wz3flaw3biw41zfi"))))
+ "033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.36.4")
+ (version "1.38.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "050q1rv04w31168ljr975vxva31n9lqdx84rnmsk6zcr6p640ffp"))))
+ "1sjn3976f1sqvrq6jq2hgc60ffxgfr3jlklaxfrk3xad5cv2kr2d"))))
(build-system r-build-system)
(arguments
`(#:phases
(add-after 'unpack 'use-system-zlib
(lambda _
(substitute* "DESCRIPTION"
- (("zlibbioc, ") ""))
+ ((" zlibbioc,") ""))
(substitute* "NAMESPACE"
(("import\\(zlibbioc\\)") ""))
#t)))))
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.28.4")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "01ylvg275iy0cvsbxkbfxcf9pi9al597v5wnlqi2xdpmrcxyc3q0"))))
+ "1khjvq1ffhqavkwf8n7bilknci60lxbg52icrcf2vnb9k8rlpghs"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
("r-iranges" ,r-iranges)
("r-rcurl" ,r-rcurl)
("r-rsqlite" ,r-rsqlite)
+ ("r-rmysql" ,r-rmysql)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
(define-public r-go-db
(package
(name "r-go-db")
- (version "3.4.0")
+ (version "3.5.0")
(source (origin
(method url-fetch)
(uri (string-append "https://www.bioconductor.org/packages/"
version ".tar.gz"))
(sha256
(base32
- "02cj8kqi5w39jwcs8gp1dgj08sah262ppxnkz4h3qd0w191y8yyl"))))
+ "02d1mn1al3q7qvhx1ylrr3ar4w4iw0qyi5d89v2336rzwk9maq35"))))
(properties
`((upstream-name . "GO.db")))
(build-system r-build-system)
(define-public r-genomationdata
(package
(name "r-genomationdata")
- (version "1.6.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"genomationData_" version ".tar.gz"))
(sha256
(base32
- "16dqwb7wx1igx77zdbcskx5m1hs4g4gp2hl56zzm70hcagnlkz8y"))))
+ "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
(build-system r-build-system)
;; As this package provides little more than large data files, it doesn't
;; make sense to build substitutes.
(define-public r-org-hs-eg-db
(package
(name "r-org-hs-eg-db")
- (version "3.4.0")
+ (version "3.5.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"org.Hs.eg.db_" version ".tar.gz"))
(sha256
(base32
- "19mg64pw8zcvb9yxzzyf7caz1kvdrkfsj1hd84bzq7crrh8kc4y6"))))
+ "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
(properties
`((upstream-name . "org.Hs.eg.db")))
(build-system r-build-system)
(home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
(synopsis "Genome wide annotation for Human")
(description
- "This package provides mappings from Entrez gene identifiers to various
-annotations for the human genome.")
+ "This package contains genome-wide annotations for Human, primarily based
+on mapping using Entrez Gene identifiers.")
(license license:artistic2.0)))
(define-public r-org-ce-eg-db
(package
(name "r-org-ce-eg-db")
- (version "3.4.0")
+ (version "3.5.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"org.Ce.eg.db_" version ".tar.gz"))
(sha256
(base32
- "12llfzrrc09kj2wzbisdspv38qzkzgpsbn8kv7qkwg746k3pq436"))))
+ "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
(properties
`((upstream-name . "org.Ce.eg.db")))
(build-system r-build-system)
(define-public r-org-dm-eg-db
(package
(name "r-org-dm-eg-db")
- (version "3.4.0")
+ (version "3.5.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"org.Dm.eg.db_" version ".tar.gz"))
(sha256
(base32
- "1vzbphbrh1cf7xi5cksia9xy9a9l42js2z2qsajvjxvddiphrb7j"))))
+ "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
(properties
`((upstream-name . "org.Dm.eg.db")))
(build-system r-build-system)
(define-public r-org-mm-eg-db
(package
(name "r-org-mm-eg-db")
- (version "3.4.0")
+ (version "3.5.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"org.Mm.eg.db_" version ".tar.gz"))
(sha256
(base32
- "1lykjqjaf01fmgg3cvfcvwd5xjq6zc5vbxnm5r4l32fzvl89q50c"))))
+ "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
(properties
`((upstream-name . "org.Mm.eg.db")))
(build-system r-build-system)
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
- (version "1.2.1")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
- "1s50diwh1j6vg3mgahh6bczvq74mfdbmwjrad4d5lh723gnc5pjg"))))
+ "08ay9h5cqsi8ypb6r0g4rfa5l1g06jgfzl64wmhgz134yqbl7vfv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-plyr" ,r-plyr)
("r-pracma" ,r-pracma)
("r-reshape2" ,r-reshape2)
+ ("r-cowplot" ,r-cowplot)
+ ("r-ggdendro" ,r-ggdendro)
+ ("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-variantannotation" ,r-variantannotation)))
(home-page "https://bioconductor.org/packages/MutationalPatterns/")
(lambda* (#:key outputs #:allow-other-keys)
(system* "tar" "-xzvf"
"src/hdf5source/hdf5small.tgz" "-C" "src/" )
- (substitute* "src/Makevars"
- (("^.*cd hdf5source &&.*$") "")
- (("^.*gunzip -dc hdf5small.tgz.*$") "")
- (("^.*rm -rf hdf5.*$") "")
- (("^.*mv hdf5source/hdf5 ..*$") ""))
(substitute* "src/hdf5/configure"
(("/bin/mv") "mv"))
#t)))))
(define-public r-chipseq
(package
(name "r-chipseq")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chipseq" version))
(sha256
(base32
- "1hahyqiwb2ch8214xqpw0c3jpiwkmyf3dwz0xc87jx6cdnzipj3i"))))
+ "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
("r-s4vectors" ,r-s4vectors)
("r-shortread" ,r-shortread)))
(home-page "https://bioconductor.org/packages/chipseq")
("r-zlibbioc" ,r-zlibbioc)))
(inputs
`(("zlib" ,zlib)))
- (home-page "http://code.google.com/p/methylkit/")
+ (home-page "https://github.com/al2na/methylKit")
(synopsis
"DNA methylation analysis from high-throughput bisulfite sequencing results")
(description
(define-public r-maldiquant
(package
(name "r-maldiquant")
- (version "1.16.4")
+ (version "1.17")
(source
(origin
(method url-fetch)
(uri (cran-uri "MALDIquant" version))
(sha256
(base32
- "1pmhsfvd45a44xdiml4zx3zd5fhygqyziqvygahkk9yibnyhv4cv"))))
+ "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z"))))
(properties `((upstream-name . "MALDIquant")))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/MALDIquant")
(define-public r-mzr
(package
(name "r-mzr")
- (version "2.10.0")
+ (version "2.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzR" version))
(sha256
(base32
- "1zir46h320n2vbrky6q3m8l221f3wdjlfsnx4ak9xca5min24xm7"))))
+ "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "src/boost")
+ #t))))
(properties `((upstream-name . "mzR")))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-boost
+ (lambda _
+ (substitute* "src/Makevars"
+ (("\\./boost/libs.*") "")
+ (("ARCH_OBJS=" line)
+ (string-append line
+ "\nARCH_LIBS=-lboost_system -lboost_regex \
+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
+ #t)))))
(inputs
- `(("boost" ,boost)
+ `(("boost" ,boost) ; use this instead of the bundled boost sources
("netcdf" ,netcdf)))
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-mzid
(package
(name "r-mzid")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzID" version))
(sha256
(base32
- "11xnild02jz24vbsfy92lb7jlqqwnrswg66a7r4rsw8d2ibrbk33"))))
+ "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9"))))
(properties `((upstream-name . "mzID")))
(build-system r-build-system)
(propagated-inputs
(define-public r-msnbase
(package
(name "r-msnbase")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnbase" version))
(sha256
(base32
- "1n9bbdlp8d8bx2mqby0c4yylz1yil42scbkxqgyrfr9s5sn6dqff"))))
+ "0dqfimljhrx3gac8d1k72gppx27lz8yckyb12v4604nbviw7xd3r"))))
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
("r-ggplot2" ,r-ggplot2)
("r-impute" ,r-impute)
("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
("r-maldiquant" ,r-maldiquant)
("r-mzid" ,r-mzid)
("r-mzr" ,r-mzr)
("r-preprocesscore" ,r-preprocesscore)
("r-protgenerics" ,r-protgenerics)
("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)
("r-s4vectors" ,r-s4vectors)
("r-vsn" ,r-vsn)
("r-xml" ,r-xml)))
(define-public r-msnid
(package
(name "r-msnid")
- (version "1.11.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
- "1vi4ngwbayrv2jkfb4pbmdp37xn04y07rh1jcklqfh0fcrm1jdig"))))
+ "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs
(license license:artistic2.0)))
(define-public r-seurat
- ;; Source releases are only made for new x.0 versions. All newer versions
- ;; are only released as pre-built binaries. At the time of this writing the
- ;; latest binary release is 1.4.0.12, which is equivalent to this commit.
- (let ((commit "fccb77d1452c35ee47e47ebf8e87bddb59f3b08d")
- (revision "1"))
- (package
- (name "r-seurat")
- (version (string-append "1.4.0.12-" revision "." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/satijalab/seurat")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "101wq3aqrdmbfi3lqmq4iivk9iwbf10d4z216ss25hf7n9091cyl"))
- ;; Delete pre-built jar.
- (snippet
- '(begin (delete-file "inst/java/ModularityOptimizer.jar")
- #t))))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'build-jar
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((classesdir "tmp-classes"))
- (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
- (mkdir classesdir)
- (and (zero? (apply system* `("javac" "-d" ,classesdir
- ,@(find-files "java" "\\.java$"))))
- (zero? (system* "jar"
- "-cf" "inst/java/ModularityOptimizer.jar"
- "-C" classesdir ".")))))))))
- (native-inputs
- `(("jdk" ,icedtea "jdk")))
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-caret" ,r-caret)
- ("r-cowplot" ,r-cowplot)
- ("r-dplyr" ,r-dplyr)
- ("r-fastica" ,r-fastica)
- ("r-fnn" ,r-fnn)
- ("r-fpc" ,r-fpc)
- ("r-gdata" ,r-gdata)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gplots" ,r-gplots)
- ("r-gridextra" ,r-gridextra)
- ("r-igraph" ,r-igraph)
- ("r-irlba" ,r-irlba)
- ("r-lars" ,r-lars)
- ("r-mixtools" ,r-mixtools)
- ("r-pbapply" ,r-pbapply)
- ("r-plyr" ,r-plyr)
- ("r-ranger" ,r-ranger)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-rcppprogress" ,r-rcppprogress)
- ("r-reshape2" ,r-reshape2)
- ("r-rocr" ,r-rocr)
- ("r-rtsne" ,r-rtsne)
- ("r-stringr" ,r-stringr)
- ("r-tclust" ,r-tclust)
- ("r-tsne" ,r-tsne)
- ("r-vgam" ,r-vgam)))
- (home-page "http://www.satijalab.org/seurat")
- (synopsis "Seurat is an R toolkit for single cell genomics")
- (description
- "This package is an R package designed for QC, analysis, and
+ (package
+ (name "r-seurat")
+ (version "2.1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "Seurat" version))
+ (sha256
+ (base32
+ "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x"))
+ ;; Delete pre-built jar.
+ (snippet
+ '(begin (delete-file "inst/java/ModularityOptimizer.jar")
+ #t))))
+ (properties `((upstream-name . "Seurat")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'build-jar
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((classesdir "tmp-classes"))
+ (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+ (mkdir classesdir)
+ (with-output-to-file "manifest"
+ (lambda _
+ (display "Manifest-Version: 1.0
+Main-Class: ModularityOptimizer\n")))
+ (and (zero? (apply system* `("javac" "-d" ,classesdir
+ ,@(find-files "java" "\\.java$"))))
+ (zero? (system* "jar"
+ "-cmf" "manifest"
+ "inst/java/ModularityOptimizer.jar"
+ "-C" classesdir ".")))))))))
+ (native-inputs
+ `(("jdk" ,icedtea "jdk")))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-caret" ,r-caret)
+ ("r-cowplot" ,r-cowplot)
+ ("r-diffusionmap" ,r-diffusionmap)
+ ("r-dplyr" ,r-dplyr)
+ ("r-dtw" ,r-dtw)
+ ("r-fnn" ,r-fnn)
+ ("r-fpc" ,r-fpc)
+ ("r-gdata" ,r-gdata)
+ ("r-ggjoy" ,r-ggjoy)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gplots" ,r-gplots)
+ ("r-gridextra" ,r-gridextra)
+ ("r-hmisc" ,r-hmisc)
+ ("r-ica" ,r-ica)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-lars" ,r-lars)
+ ("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-mixtools" ,r-mixtools)
+ ("r-nmf" ,r-nmf)
+ ("r-pbapply" ,r-pbapply)
+ ("r-plotly" ,r-plotly)
+ ("r-ranger" ,r-ranger)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppprogress" ,r-rcppprogress)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rocr" ,r-rocr)
+ ("r-rtsne" ,r-rtsne)
+ ("r-sdmtools" ,r-sdmtools)
+ ("r-stringr" ,r-stringr)
+ ("r-tclust" ,r-tclust)
+ ("r-tidyr" ,r-tidyr)
+ ("r-tsne" ,r-tsne)
+ ("r-vgam" ,r-vgam)))
+ (home-page "http://www.satijalab.org/seurat")
+ (synopsis "Seurat is an R toolkit for single cell genomics")
+ (description
+ "This package is an R package designed for QC, analysis, and
exploration of single cell RNA-seq data. It easily enables widely-used
analytical techniques, including the identification of highly variable genes,
dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
algorithms; density clustering, hierarchical clustering, k-means, and the
discovery of differentially expressed genes and markers.")
- (license license:gpl3))))
+ (license license:gpl3)))
(define-public r-aroma-light
(package
(define-public r-annotationhub
(package
(name "r-annotationhub")
- (version "2.8.2")
+ (version "2.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
- "1nh5si3j1nv37jcg4260582ayjg18851np47cskrm54prnvhwd9r"))))
+ "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biocgenerics" ,r-biocgenerics)
("r-biocinstaller" ,r-biocinstaller)
+ ("r-curl" ,r-curl)
("r-httr" ,r-httr)
("r-interactivedisplaybase" ,r-interactivedisplaybase)
("r-rsqlite" ,r-rsqlite)
microarrays or GRanges for sequencing data.")
(license license:lgpl2.0+)))
-(define-public r-qvalue
+(define-public r-keggrest
(package
- (name "r-qvalue")
- (version "2.10.0")
+ (name "r-keggrest")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
- (uri (bioconductor-uri "qvalue" version))
+ (uri (bioconductor-uri "KEGGREST" version))
(sha256
(base32
- "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i"))))
+ "1i3i88lj57wvpgjf75a23msgfsjv8pr2b4j1faga276p4fsblkhj"))))
+ (properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
- `(("r-ggplot2" ,r-ggplot2)
- ("r-reshape2" ,r-reshape2)))
- (home-page "http://github.com/jdstorey/qvalue")
- (synopsis "Q-value estimation for false discovery rate control")
+ `(("r-biostrings" ,r-biostrings)
+ ("r-httr" ,r-httr)
+ ("r-png" ,r-png)))
+ (home-page "https://bioconductor.org/packages/KEGGREST")
+ (synopsis "Client-side REST access to KEGG")
(description
- "This package takes a list of p-values resulting from the simultaneous
-testing of many hypotheses and estimates their q-values and local @dfn{false
-discovery rate} (FDR) values. The q-value of a test measures the proportion
-of false positives incurred when that particular test is called significant.
-The local FDR measures the posterior probability the null hypothesis is true
-given the test's p-value. Various plots are automatically generated, allowing
-one to make sensible significance cut-offs. The software can be applied to
-problems in genomics, brain imaging, astrophysics, and data mining.")
- ;; Any version of the LGPL.
- (license license:lgpl3+)))
+ "This package provides a package that provides a client interface to the
+@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
+ (license license:artistic2.0)))
-(define htslib-for-sambamba
- (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
- (package
- (inherit htslib)
- (name "htslib-for-sambamba")
- (version (string-append "1.3.1-1." (string-take commit 9)))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/lomereiter/htslib.git")
+(define-public r-gage
+ (package
+ (name "r-gage")
+ (version "2.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gage" version))
+ (sha256
+ (base32
+ "1r14p88q3y736pkqm4pdimf1izy1xy3xgivmj3cr4dv65kjny1zk"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-graph" ,r-graph)
+ ("r-keggrest" ,r-keggrest)))
+ (home-page "http://www.biomedcentral.com/1471-2105/10/161")
+ (synopsis "Generally applicable gene-set enrichment for pathway analysis")
+ (description
+ "GAGE is a published method for gene set (enrichment or GSEA) or pathway
+analysis. GAGE is generally applicable independent of microarray or RNA-Seq
+data attributes including sample sizes, experimental designs, assay platforms,
+and other types of heterogeneity. The gage package provides functions for
+basic GAGE analysis, result processing and presentation. In addition, it
+provides demo microarray data and commonly used gene set data based on KEGG
+pathways and GO terms. These funtions and data are also useful for gene set
+analysis using other methods.")
+ (license license:gpl2+)))
+
+(define-public r-genomicfiles
+ (package
+ (name "r-genomicfiles")
+ (version "1.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicFiles" version))
+ (sha256
+ (base32
+ "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n"))))
+ (properties `((upstream-name . "GenomicFiles")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/GenomicFiles")
+ (synopsis "Distributed computing by file or by range")
+ (description
+ "This package provides infrastructure for parallel computations
+distributed by file or by range. User defined mapper and reducer functions
+provide added flexibility for data combination and manipulation.")
+ (license license:artistic2.0)))
+
+(define-public r-complexheatmap
+ (package
+ (name "r-complexheatmap")
+ (version "1.17.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ComplexHeatmap" version))
+ (sha256
+ (base32
+ "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy"))))
+ (properties
+ `((upstream-name . "ComplexHeatmap")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-circlize" ,r-circlize)
+ ("r-colorspace" ,r-colorspace)
+ ("r-getoptlong" ,r-getoptlong)
+ ("r-globaloptions" ,r-globaloptions)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page
+ "https://github.com/jokergoo/ComplexHeatmap")
+ (synopsis "Making Complex Heatmaps")
+ (description
+ "Complex heatmaps are efficient to visualize associations between
+different sources of data sets and reveal potential structures. This package
+provides a highly flexible way to arrange multiple heatmaps and supports
+self-defined annotation graphics.")
+ (license license:gpl2+)))
+
+(define-public r-dirichletmultinomial
+ (package
+ (name "r-dirichletmultinomial")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DirichletMultinomial" version))
+ (sha256
+ (base32
+ "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1"))))
+ (properties
+ `((upstream-name . "DirichletMultinomial")))
+ (build-system r-build-system)
+ (inputs
+ `(("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/DirichletMultinomial")
+ (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
+ (description
+ "Dirichlet-multinomial mixture models can be used to describe variability
+in microbial metagenomic data. This package is an interface to code
+originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
+1-15.")
+ (license license:lgpl3)))
+
+(define-public r-ensembldb
+ (package
+ (name "r-ensembldb")
+ (version "2.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ensembldb" version))
+ (sha256
+ (base32
+ "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("r-annotationhub" ,r-annotationhub)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-curl" ,r-curl)
+ ("r-dbi" ,r-dbi)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/jotsetung/ensembldb")
+ (synopsis "Utilities to create and use Ensembl-based annotation databases")
+ (description
+ "The package provides functions to create and use transcript-centric
+annotation databases/packages. The annotation for the databases are directly
+fetched from Ensembl using their Perl API. The functionality and data is
+similar to that of the TxDb packages from the @code{GenomicFeatures} package,
+but, in addition to retrieve all gene/transcript models and annotations from
+the database, the @code{ensembldb} package also provides a filter framework
+allowing to retrieve annotations for specific entries like genes encoded on a
+chromosome region or transcript models of lincRNA genes.")
+ ;; No version specified
+ (license license:lgpl3+)))
+
+(define-public r-organismdbi
+ (package
+ (name "r-organismdbi")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "OrganismDbi" version))
+ (sha256
+ (base32
+ "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8"))))
+ (properties `((upstream-name . "OrganismDbi")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocinstaller" ,r-biocinstaller)
+ ("r-dbi" ,r-dbi)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-graph" ,r-graph)
+ ("r-iranges" ,r-iranges)
+ ("r-rbgl" ,r-rbgl)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/OrganismDbi")
+ (synopsis "Software to enable the smooth interfacing of database packages")
+ (description "The package enables a simple unified interface to several
+annotation packages each of which has its own schema by taking advantage of
+the fact that each of these packages implements a select methods.")
+ (license license:artistic2.0)))
+
+(define-public r-biovizbase
+ (package
+ (name "r-biovizbase")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biovizBase" version))
+ (sha256
+ (base32
+ "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f"))))
+ (properties `((upstream-name . "biovizBase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dichromat" ,r-dichromat)
+ ("r-ensembldb" ,r-ensembldb)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hmisc" ,r-hmisc)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/biovizBase")
+ (synopsis "Basic graphic utilities for visualization of genomic data")
+ (description
+ "The biovizBase package is designed to provide a set of utilities, color
+schemes and conventions for genomic data. It serves as the base for various
+high-level packages for biological data visualization. This saves development
+effort and encourages consistency.")
+ (license license:artistic2.0)))
+
+(define-public r-ggbio
+ (package
+ (name "r-ggbio")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ggbio" version))
+ (sha256
+ (base32
+ "1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-biovizbase" ,r-biovizbase)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-ensembldb" ,r-ensembldb)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggally" ,r-ggally)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gtable" ,r-gtable)
+ ("r-hmisc" ,r-hmisc)
+ ("r-iranges" ,r-iranges)
+ ("r-organismdbi" ,r-organismdbi)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "http://www.tengfei.name/ggbio/")
+ (synopsis "Visualization tools for genomic data")
+ (description
+ "The ggbio package extends and specializes the grammar of graphics for
+biological data. The graphics are designed to answer common scientific
+questions, in particular those often asked of high throughput genomics data.
+All core Bioconductor data structures are supported, where appropriate. The
+package supports detailed views of particular genomic regions, as well as
+genome-wide overviews. Supported overviews include ideograms and grand linear
+views. High-level plots include sequence fragment length, edge-linked
+interval to data view, mismatch pileup, and several splicing summaries.")
+ (license license:artistic2.0)))
+
+(define-public r-gprofiler
+ (package
+ (name "r-gprofiler")
+ (version "0.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gProfileR" version))
+ (sha256
+ (base32
+ "1qix15d0wa9nspdclcawml94mng4qmr2jciv7d24py315wfsvv8p"))))
+ (properties `((upstream-name . "gProfileR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-plyr" ,r-plyr)
+ ("r-rcurl" ,r-rcurl)))
+ (home-page "http://cran.r-project.org/web/packages/gProfileR/")
+ (synopsis "Interface to the g:Profiler toolkit")
+ (description
+ "This package provides tools for functional enrichment analysis,
+gene identifier conversion and mapping homologous genes across related
+organisms via the @code{g:Profiler} toolkit.")
+ (license license:gpl2+)))
+
+(define-public r-gqtlbase
+ (package
+ (name "r-gqtlbase")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gQTLBase" version))
+ (sha256
+ (base32
+ "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035"))))
+ (properties `((upstream-name . "gQTLBase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-batchjobs" ,r-batchjobs)
+ ("r-bbmisc" ,r-bbmisc)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-bit" ,r-bit)
+ ("r-doparallel" ,r-doparallel)
+ ("r-ff" ,r-ff)
+ ("r-ffbase" ,r-ffbase)
+ ("r-foreach" ,r-foreach)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/gQTLBase")
+ (synopsis "Infrastructure for eQTL, mQTL and similar studies")
+ (description
+ "The purpose of this package is to simplify the storage and interrogation
+of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
+and more.")
+ (license license:artistic2.0)))
+
+(define-public r-snpstats
+ (package
+ (name "r-snpstats")
+ (version "1.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "snpStats" version))
+ (sha256
+ (base32
+ "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir"))))
+ (properties `((upstream-name . "snpStats")))
+ (build-system r-build-system)
+ (inputs `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-matrix" ,r-matrix)
+ ("r-survival" ,r-survival)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "https://bioconductor.org/packages/snpStats")
+ (synopsis "Methods for SNP association studies")
+ (description
+ "This package provides classes and statistical methods for large
+@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
+the earlier snpMatrix package, allowing for uncertainty in genotypes.")
+ (license license:gpl3)))
+
+(define-public r-homo-sapiens
+ (package
+ (name "r-homo-sapiens")
+ (version "1.3.1")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "http://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "Homo.sapiens_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
+ (properties
+ `((upstream-name . "Homo.sapiens")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-go-db" ,r-go-db)
+ ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+ ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
+ ("r-organismdbi" ,r-organismdbi)
+ ("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://bioconductor.org/packages/Homo.sapiens/")
+ (synopsis "Annotation package for the Homo.sapiens object")
+ (description
+ "This package contains the Homo.sapiens object to access data from
+several related annotation packages.")
+ (license license:artistic2.0)))
+
+(define-public r-erma
+ (package
+ (name "r-erma")
+ (version "0.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "erma" version))
+ (sha256
+ (base32
+ "0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-foreach" ,r-foreach)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-homo-sapiens" ,r-homo-sapiens)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/erma")
+ (synopsis "Epigenomic road map adventures")
+ (description
+ "The epigenomics road map describes locations of epigenetic marks in DNA
+from a variety of cell types. Of interest are locations of histone
+modifications, sites of DNA methylation, and regions of accessible chromatin.
+This package presents a selection of elements of the road map including
+metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
+by Ernst and Kellis.")
+ (license license:artistic2.0)))
+
+(define-public r-ldblock
+ (package
+ (name "r-ldblock")
+ (version "1.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ldblock" version))
+ (sha256
+ (base32
+ "18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-erma" ,r-erma)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-go-db" ,r-go-db)
+ ("r-homo-sapiens" ,r-homo-sapiens)
+ ("r-matrix" ,r-matrix)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-snpstats" ,r-snpstats)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/ldblock")
+ (synopsis "Data structures for linkage disequilibrium measures in populations")
+ (description
+ "This package defines data structures for @dfn{linkage
+disequilibrium} (LD) measures in populations. Its purpose is to simplify
+handling of existing population-level data for the purpose of flexibly
+defining LD blocks.")
+ (license license:artistic2.0)))
+
+(define-public r-gqtlstats
+ (package
+ (name "r-gqtlstats")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gQTLstats" version))
+ (sha256
+ (base32
+ "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq"))))
+ (properties `((upstream-name . "gQTLstats")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-batchjobs" ,r-batchjobs)
+ ("r-bbmisc" ,r-bbmisc)
+ ("r-beeswarm" ,r-beeswarm)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-doparallel" ,r-doparallel)
+ ("r-dplyr" ,r-dplyr)
+ ("r-erma" ,r-erma)
+ ("r-ffbase" ,r-ffbase)
+ ("r-foreach" ,r-foreach)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbeeswarm" ,r-ggbeeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gqtlbase" ,r-gqtlbase)
+ ("r-hardyweinberg" ,r-hardyweinberg)
+ ("r-iranges" ,r-iranges)
+ ("r-ldblock" ,r-ldblock)
+ ("r-limma" ,r-limma)
+ ("r-mgcv" ,r-mgcv)
+ ("r-plotly" ,r-plotly)
+ ("r-reshape2" ,r-reshape2)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-snpstats" ,r-snpstats)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/gQTLstats")
+ (synopsis "Computationally efficient analysis for eQTL and allied studies")
+ (description
+ "This package provides tools for the computationally efficient analysis
+of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
+The software in this package aims to support refinements and functional
+interpretation of members of a collection of association statistics on a
+family of feature/genome hypotheses.")
+ (license license:artistic2.0)))
+
+(define-public r-gviz
+ (package
+ (name "r-gviz")
+ (version "1.22.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Gviz" version))
+ (sha256
+ (base32
+ "173n99mc95sij2vb8n3xd016x7mxhjs961q3l29xkg1lrnnm2sva"))))
+ (properties `((upstream-name . "Gviz")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
+ ("r-biovizbase" ,r-biovizbase)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-digest" ,r-digest)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/Gviz")
+ (synopsis "Plotting data and annotation information along genomic coordinates")
+ (description
+ "Genomic data analyses requires integrated visualization of known genomic
+information and new experimental data. Gviz uses the biomaRt and the
+rtracklayer packages to perform live annotation queries to Ensembl and UCSC
+and translates this to e.g. gene/transcript structures in viewports of the
+grid graphics package. This results in genomic information plotted together
+with your data.")
+ (license license:artistic2.0)))
+
+(define-public r-gwascat
+ (package
+ (name "r-gwascat")
+ (version "2.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gwascat" version))
+ (sha256
+ (base32
+ "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationhub" ,r-annotationhub)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gqtlstats" ,r-gqtlstats)
+ ("r-graph" ,r-graph)
+ ("r-gviz" ,r-gviz)
+ ("r-homo-sapiens" ,r-homo-sapiens)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-snpstats" ,r-snpstats)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/gwascat")
+ (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
+ (description
+ "This package provides tools for representing and modeling data in the
+EMBL-EBI GWAS catalog.")
+ (license license:artistic2.0)))
+
+(define-public r-sushi
+ (package
+ (name "r-sushi")
+ (version "1.16.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Sushi" version))
+ (sha256
+ (base32
+ "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g"))))
+ (properties `((upstream-name . "Sushi")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biomart" ,r-biomart)
+ ("r-zoo" ,r-zoo)))
+ (home-page "https://bioconductor.org/packages/Sushi")
+ (synopsis "Tools for visualizing genomics data")
+ (description
+ "This package provides flexible, quantitative, and integrative genomic
+visualizations for publication-quality multi-panel figures.")
+ (license license:gpl2+)))
+
+(define-public r-fithic
+ (package
+ (name "r-fithic")
+ (version "1.4.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "FitHiC" version))
+ (sha256
+ (base32
+ "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n"))))
+ (properties `((upstream-name . "FitHiC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-fdrtool" ,r-fdrtool)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://bioconductor.org/packages/FitHiC")
+ (synopsis "Confidence estimation for intra-chromosomal contact maps")
+ (description
+ "Fit-Hi-C is a tool for assigning statistical confidence estimates to
+intra-chromosomal contact maps produced by genome-wide genome architecture
+assays such as Hi-C.")
+ (license license:gpl2+)))
+
+(define-public r-hitc
+ (package
+ (name "r-hitc")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HiTC" version))
+ (sha256
+ (base32
+ "0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp"))))
+ (properties `((upstream-name . "HiTC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rtracklayer" ,r-rtracklayer)))
+ (home-page "https://bioconductor.org/packages/HiTC")
+ (synopsis "High throughput chromosome conformation capture analysis")
+ (description
+ "The HiTC package was developed to explore high-throughput \"C\" data
+such as 5C or Hi-C. Dedicated R classes as well as standard methods for
+quality controls, normalization, visualization, and further analysis are also
+provided.")
+ (license license:artistic2.0)))
+
+(define-public r-qvalue
+ (package
+ (name "r-qvalue")
+ (version "2.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "qvalue" version))
+ (sha256
+ (base32
+ "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-reshape2" ,r-reshape2)))
+ (home-page "http://github.com/jdstorey/qvalue")
+ (synopsis "Q-value estimation for false discovery rate control")
+ (description
+ "This package takes a list of p-values resulting from the simultaneous
+testing of many hypotheses and estimates their q-values and local @dfn{false
+discovery rate} (FDR) values. The q-value of a test measures the proportion
+of false positives incurred when that particular test is called significant.
+The local FDR measures the posterior probability the null hypothesis is true
+given the test's p-value. Various plots are automatically generated, allowing
+one to make sensible significance cut-offs. The software can be applied to
+problems in genomics, brain imaging, astrophysics, and data mining.")
+ ;; Any version of the LGPL.
+ (license license:lgpl3+)))
+
+(define htslib-for-sambamba
+ (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
+ (package
+ (inherit htslib)
+ (name "htslib-for-sambamba")
+ (version (string-append "1.3.1-1." (string-take commit 9)))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/lomereiter/htslib.git")
(commit commit)))
(file-name (string-append "htslib-" version "-checkout"))
(sha256
using nucleotide or amino-acid sequence data.")
;; GPLv3 only
(license license:gpl3)))
+
+(define-public kallisto
+ (package
+ (name "kallisto")
+ (version "0.43.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/pachterlab/"
+ "kallisto/archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11"))))
+ (build-system cmake-build-system)
+ (arguments `(#:tests? #f)) ; no "check" target
+ (inputs
+ `(("hdf5" ,hdf5)
+ ("zlib" ,zlib)))
+ (home-page "http://pachterlab.github.io/kallisto/")
+ (synopsis "Near-optimal RNA-Seq quantification")
+ (description
+ "Kallisto is a program for quantifying abundances of transcripts from
+RNA-Seq data, or more generally of target sequences using high-throughput
+sequencing reads. It is based on the novel idea of pseudoalignment for
+rapidly determining the compatibility of reads with targets, without the need
+for alignment. Pseudoalignment of reads preserves the key information needed
+for quantification, and kallisto is therefore not only fast, but also as
+accurate as existing quantification tools.")
+ (license license:bsd-2)))