Annotation and SeqFeature objects and databases, Blast objects can be
converted to Alignment objects, and so on. This means that the objects
provide a coordinated and extensible framework to do computational biology.")
- (license (package-license perl)))))
+ (license license:perl-license))))
(define-public python-biopython
(package
(setenv "HOME" "/tmp")
(and (zero? (system* "make" "-C" "pysam_data"))
(zero? (system* "make" "-C" "cbcf_data"))
- (zero? (system* "nosetests" "-v"
- "--processes"
- (number->string (parallel-job-count)))))))))))
+ ;; Running nosetests without explicitly asking for a
+ ;; single process leads to a crash. Running with multiple
+ ;; processes fails because the tests are not designed to
+ ;; run in parallel.
+
+ ;; FIXME: tests keep timing out on some systems.
+ ;; (zero? (system* "nosetests" "-v"
+ ;; "--processes" "1"))
+ )))))))
(propagated-inputs
`(("htslib" ,htslib))) ; Included from installed header files.
(inputs
(define-public diamond
(package
(name "diamond")
- (version "0.8.37")
+ (version "0.8.38")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1zn7q8m41ayfnjvf9snrsnq00mm68alf9rhdadx5q1sk23lyvp2l"))))
+ "0q2z6z5f7c0kbbzpjamkcyqg0rc6h5rxfp97qbmb0wxaycr7jajq"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
reads at a typical sensitivity of 90-99% relative to BLAST depending on the
data and settings.")
- ;; diamond fails to build on other platforms
- ;; https://github.com/bbuchfink/diamond/issues/18
- (supported-systems '("x86_64-linux"))
(license (license:non-copyleft "file://src/COPYING"
"See src/COPYING in the distribution."))))
(define-public mafft
(package
(name "mafft")
- (version "7.305")
+ (version "7.310")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tgz"))
(sha256
(base32
- "0ziim7g58n3z8gppsa713f5fxprl60ldj3xck186z0n9dpp06i8r"))))
+ "0gbsaz6z2qa307kd7wfb06c3y4ikmv1hsdvlns11f6zq4w1z9pwc"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no automated tests, though there are tests in the read me
(define-public proteinortho
(package
(name "proteinortho")
- (version "5.15")
+ (version "5.16")
(source
(origin
(method url-fetch)
version "_src.tar.gz"))
(sha256
(base32
- "05wacnnbx56avpcwhzlcf6b7s77swcpv3qnwz5sh1z54i51gg2ki"))))
+ "0z4f5cg0cs8ai62hfvp4q6w66q2phcc55nhs4xj5cyhxxivjv2ai"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
(define-public raxml
(package
(name "raxml")
- (version "8.2.9")
+ (version "8.2.10")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7"))))
+ "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests.
(define-public vcftools
(package
(name "vcftools")
- (version "0.1.14")
+ (version "0.1.15")
(source (origin
(method url-fetch)
(uri (string-append
version "/vcftools-" version ".tar.gz"))
(sha256
(base32
- "10l5c07z9p4i9pr4gl54b2c9h6ndhqlbq1rashg2zcgwkbfrkmvn"))))
+ "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
(define-public r-vegan
(package
(name "r-vegan")
- (version "2.4-2")
+ (version "2.4-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "vegan" version))
(sha256
(base32
- "12wf64izrpq9z3ix7mgm5421mq0xsm8dw5qblvcrz452nfhjf5w9"))))
+ "15zcxfix2d854897k1lr0sfmj2n00339nlsppcr3zrb238lb2mi5"))))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'revert-test-deletion
- ;; The distributed sources do not include tests with the CRAN
- ;; package. Here we revert the commit
- ;; `591d0e8ba1deaaf82445474ec6619c0b43db4e63' which deletes these
- ;; tests. There are plans to not delete tests in future as
- ;; documented at https://github.com/vegandevs/vegan/issues/181.
- (lambda* (#:key inputs #:allow-other-keys)
- (zero?
- (system* "patch" "-R" "-p1" "-i"
- (assoc-ref inputs "r-vegan-delete-tests-patch"))))))))
(native-inputs
`(("gfortran" ,gfortran)
- ("r-knitr" ,r-knitr)
- ("r-vegan-delete-tests-patch"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/vegandevs/vegan/commit/"
- "591d0e8ba1deaaf82445474ec6619c0b43db4e63.patch"))
- (sha256
- (base32
- "0b1bi7y4jjdl3ph721vm9apm51dr2z9piwvhy4355sf2b4kyyj5a"))))))
+ ("r-knitr" ,r-knitr)))
(propagated-inputs
`(("r-cluster" ,r-cluster)
("r-lattice" ,r-lattice)
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.52.1")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "0yymz8qxgnbybvfhqrgkd1hh9dhwxdii1yxkhr1zicjgb35xixxb"))))
+ "03hmbvp3i6lvd307fqdg7akxi2qp322rlky3bzw0zccgm0i0221g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(home-page
"http://bioconductor.org/packages/annotate")
(synopsis "Annotation for microarrays")
- (description "This package provides R enviroments for the annotation of
+ (description "This package provides R environments for the annotation of
microarrays.")
(license license:artistic2.0)))
(define-public r-geneplotter
(package
(name "r-geneplotter")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneplotter" version))
(sha256
(base32
- "1p6yvxi243irhjxwm97hp73abhwampj0myyf8z00ij166674pc7h"))))
+ "0a0ajns21db5rrjl16bq6wawggsnxr00fg184pc38nmfghv4z4b6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
(define-public r-genefilter
(package
(name "r-genefilter")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "genefilter" version))
(sha256
(base32
- "1vzgciqd09csqcw9qync8blsv51ylrd86a65iadgyy6j26g01fwd"))))
+ "0sf2hdi9nv6r83vn1y65m4jiba8pffddpj46d6yjn5rlsixplmqg"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.14.1")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "1walwkqryn1gnwz7zryr5764a0p6ia7ag4w6w9n8fskg8dkg0fqs"))))
+ "0m0apn3xi4kdkinsj4xkw5cwysicyjr6xxlxhpa4scyv589am1s5"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'link-against-armadillo
- (lambda _
- (substitute* "src/Makevars"
- (("PKG_LIBS =" prefix)
- (string-append prefix "-larmadillo"))))))))
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf"))))
+ "01kd86vvgpa4a5zivcy4g6z8rhcykasdskrz8yqsqz211sd1xsr3"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
(define-public r-rbgl
(package
(name "r-rbgl")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RBGL" version))
(sha256
(base32
- "1q14m8w6ih56v680kf3d9wh1qbgp7af33kz3cxafdf1vvzx9km08"))))
+ "11db6kvz453ypj9ds3xpjqzwrrjck84ijn4wlhkfyz2dzdgd5ryv"))))
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
(propagated-inputs `(("r-graph" ,r-graph)))
(define-public r-gseabase
(package
(name "r-gseabase")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "0l2x7yj7lfb0m2dmsav5ib026dikpgl4crdckrnj776yy08lgxpj"))))
+ "1c6i6g4fj3b8wjyxyygr7i3v8sxrq1ffb2bbicya5ah2gdaclfad"))))
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-category
(package
(name "r-category")
- (version "2.40.0")
+ (version "2.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Category" version))
(sha256
(base32
- "16ncwz7b4y48k0p3fvbrbmvf7nfz63li9ysgcl8kp9kl4hg7llng"))))
+ "0swcmihyjg0fhaaydl9hm24aj9zffw3bibza9y6sqs6jaqd97f09"))))
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gostats
(package
(name "r-gostats")
- (version "2.40.0")
+ (version "2.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOstats" version))
(sha256
(base32
- "0g2czm94zhzx92z7y2r4mjfxhwml7bhab2db6820ks8nkw1zvr9n"))))
+ "0qvqjgfnd9ap4rikvyxa9p4dhcnccvkw8phzv88vghh6pq463d62"))))
(properties `((upstream-name . "GOstats")))
(build-system r-build-system)
(propagated-inputs
(define-public r-shortread
(package
(name "r-shortread")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
- "0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls"))))
+ "0ayk3d5625ymb5g2gycq6banzqmyd642xrwjzhdshz2dwid7kly8"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
(define-public r-systempiper
(package
(name "r-systempiper")
- (version "1.8.1")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
- "0hyi841w8fm2yzpm6lwqi3jz5kc8ny8dy5p29dxynzaw5bpjw56d"))))
+ "0c3m5rq63ypv15yca97yag5d4vgd7xj9by2a4sd8z0pcmpajz0hw"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-grohmm
(package
(name "r-grohmm")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "groHMM" version))
(sha256
(base32
- "0d91nyhqbi5hv3mgmr2z0g29wg2md26g0hyv5mgapmz20cd9zi4y"))))
+ "16k1kp4sbhh0vp7dzywafq52csq42ksqfrqfy4bdv1qbd7536dpd"))))
(properties `((upstream-name . "groHMM")))
(build-system r-build-system)
(propagated-inputs
(define-public vsearch
(package
(name "vsearch")
- (version "2.4.2")
+ (version "2.4.3")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "15zy2d9xvgbgdjlxvrhj8s5ga42p13k7a3xv015ingn0bi1p3n6w"))
+ "0hc110ycqpa54nr6x173qg7190hk08qp7yz7zzqxlsypqnpc5zzp"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
- (version "0.20.0")
+ (version "0.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocGenerics" version))
(sha256
(base32
- "06szdz7dfs1iyv5zdl4fjzad18nnf1zf3wvglc6c6yd9mrqlf7vk"))))
+ "0qbmz2qxwwi30xpxpvp2h1h7l494rbbz5d9pls5cfhqdv3wnpzsv"))))
(properties
`((upstream-name . "BiocGenerics")))
(build-system r-build-system)
(define-public r-biocinstaller
(package
(name "r-biocinstaller")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocInstaller" version))
(sha256
(base32
- "0y1y5wmy6lzjqx3hdg15n91d417ccjj8dbvdkhmp99bs5aijwcpn"))))
+ "0njw2q3lq1rrjx8qzw5d2130l72bmd3g2z8qlxqmkdcbmmgliyj2"))))
(properties
`((upstream-name . "BiocInstaller")))
(build-system r-build-system)
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.42.0")
+ (version "1.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "07rjk10b91pkriyq297w86199r2d3sfji3ggs9mq2gyalsa8y4b6"))))
+ "17hi8w0w63f5yc43kid5pbld3ca78sj6n8x9dmkbl8h48818xbga"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
also known as views, in a controlled vocabulary.")
(license license:artistic2.0)))
+(define-public r-bookdown
+ (package
+ (name "r-bookdown")
+ (version "0.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "bookdown" version))
+ (sha256
+ (base32
+ "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-htmltools" ,r-htmltools)
+ ("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://github.com/rstudio/bookdown")
+ (synopsis "Authoring books and technical documents with R markdown")
+ (description "This package provides output formats and utilities for
+authoring books and technical documents with R Markdown.")
+ (license license:gpl3)))
+
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.2.1")
+ (version "2.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "0sl99xw940ixrm6v24lgaw3ljh56g59a6rdz7g160hx84z9f8n2n"))))
+ "1n2c8rj920wmk3q2khmjfnhn5i4b3lmhx1whnghk0zk3jf88hvbi"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
+ (propagated-inputs
+ `(("r-bookdown" ,r-bookdown)
+ ("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-yaml" ,r-yaml)))
(home-page "http://bioconductor.org/packages/BiocStyle")
(synopsis "Bioconductor formatting styles")
(description "This package provides standard formatting styles for
(define-public r-bioccheck
(package
(name "r-bioccheck")
- (version "1.10.1")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
- "197kpiycyl3qawm6801fxyxj81d2g57a00qxaqprapsf1d140l52"))))
+ "01zkw5hggzvn0wj4msac71k1mknq4h2inn1c2hwqgw4cy1675wl0"))))
(properties
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
(define-public r-dnacopy
(package
(name "r-dnacopy")
- (version "1.48.0")
+ (version "1.50.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DNAcopy" version))
(sha256
(base32
- "1idyvfvy7xx8k9vk00y4k3819qmip8iqm809j3vpxabmsn7r9zyh"))))
+ "0112ry62z18m7rdyrn3gvbxq2f6m44cawhcfb1f02z9xzlsj0k28"))))
(properties
`((upstream-name . "DNAcopy")))
(build-system r-build-system)
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.12.1")
+ (version "0.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0i36y3w36h3d8rmazxcrip4gvn54rd9av1wz4lygsprrjmylfhcc"))))
+ "0ywwrs4d752xfk0p0w122kvi0xvp6nmxnyynchbsa8zciqymhgv8"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
(define-public r-seqinr
(package
(name "r-seqinr")
- (version "3.3-3")
+ (version "3.3-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqinr" version))
(sha256
(base32
- "0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj"))))
+ "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ade4" ,r-ade4)
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.8.2")
+ (version "2.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "0x8h74ik3xwdnwrkn89hq5ll0qa1lp9jgzlbmpa02dpws7snfwyr"))))
+ "0zp4mxm9h1p4krj7m7cinkvwa2ibqkq59jwpan97yvhb4z8q0d6n"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
possible.")
(license license:artistic2.0)))
+(define-public r-genomeinfodbdata
+ (package
+ (name "r-genomeinfodbdata")
+ (version "0.99.0")
+ (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 "https://bioconductor.org/packages/release/"
+ "data/annotation/src/contrib/GenomeInfoDbData_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "120qvhb0pvkzd65lsgja62vyrgc37si6fh68q4cg4w5x9f04jw25"))))
+ (properties
+ `((upstream-name . "GenomeInfoDbData")))
+ (build-system r-build-system)
+ (home-page "http://bioconductor.org/packages/GenomeInfoDbData")
+ (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
+ (description "This package contains data for mapping between NCBI taxonomy
+ID and species. It is used by functions in the GenomeInfoDb package.")
+ (license license:artistic2.0)))
+
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.10.3")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "18g24cf6b3vi13w85ki2mam6i2gl4yxr1zchyga34xc3dkdngzrw"))))
+ "1bwwhscjl376a5p43mx8ijrqajxmgypbqhv049pgagl22hkkf0y3"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomeinfodbdata" ,r-genomeinfodbdata)
("r-iranges" ,r-iranges)
("r-rcurl" ,r-rcurl)
("r-s4vectors" ,r-s4vectors)))
(define-public r-edger
(package
(name "r-edger")
- (version "3.16.5")
+ (version "3.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "04vpa0a6dkkjyvvfbkmfjyaxf2ldkagi66g028qpaszd8jsk8yiv"))))
+ "02l17i6xh33dv10swwvyfxrmv5kp23iv278iwvkfq2mnipasfnb9"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.20.3")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "10v8apgfw57nd4dxmdxdrijxpw135jpp2p8wrk3wjpb3hhfjp1qj"))))
+ "05hpm4as36kvpiqhgnkfjwfx0a05p304c21ggba29iac4nanm8b3"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
(define-public r-limma
(package
(name "r-limma")
- (version "3.30.13")
+ (version "3.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1ji8kb19anwq2505zii2kzqlrnk75mk1mpz8vy4s1mckzs1cz4m0"))))
+ "0q7rqm86nwq0rg4fjggfr7xqybjrxj425vni3cva70b4c8d1h425"))))
(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-xvector
(package
(name "r-xvector")
- (version "0.14.1")
+ (version "0.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "XVector" version))
(sha256
(base32
- "1j14ip4c260kdp3zcmgfa2v8ky88csa0gfdg6a1xsb64s03hdbm6"))))
+ "01n09f4jdm60684lzikp02zf9gjan8bdrjx740vggr21q9fa69wn"))))
(properties
`((upstream-name . "XVector")))
(build-system r-build-system)
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.26.4")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "1789ycqzv20d8p1axkxrhsz9v0ww6w1dk2mfvm85p8j53zd1f67c"))))
+ "10x9zx0b7j05d1j6p0xs4q4f4wzbhf3rq64wzi9cgv7f44q43a5n"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
(define-public r-biobase
(package
(name "r-biobase")
- (version "2.34.0")
+ (version "2.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biobase" version))
(sha256
(base32
- "0js9j9wqls8f571ifl9ylllbb9a9hwf7b7drf2grwb1fl31ldazl"))))
+ "0x7pf5xsdcj12dbf5qqki2c6bd5madqg2fbiq5xgisarpc9v6c1m"))))
(properties
`((upstream-name . "Biobase")))
(build-system r-build-system)
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.36.2")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "0574lmyisn3nv9aicz9x3iivx990da4q2j4i0f1jz0mpj9v3vc2w"))))
+ "1xffm98s817mfc827cnr0by6167nlrl1glxzjawzz0rkghs41g27"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.30.0")
+ (version "2.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "1x0flcghq71784q2l02j0g4f9jkmyb14f6i307n6c59d6ji7h7x6"))))
+ "0knkxh23vl9pa0by03xr6dy9aiah714cmf54jl828k51l9wv5l2j"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.8.1")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "123i928rwi4h4sy4fpysv6pinw5nns0sm3myxi2ghqhm34ws8gyl"))))
+ "01ph0kq70b5gkd7n6a4myjlvwzgc0hi4xfwz8h17h06n9p5sdwa9"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.42.1")
+ (version "2.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "0vqgd9i6y3wj4zviqwgvwgd4qj6033fg01rmx1cw9bw5i8ans42d"))))
+ "0ixgx12cx2z4n2khxq83crz9gc21qckj2v78y2p31567kfsw7clg"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "1.26.1")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck"))))
+ "1zx6vhdz3lksbfy98jj3qzl7cxgspigm2pbsd5835b12r6mc5w6d"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
files.")
(license license:expat)))
+(define-public r-delayedarray
+ (package
+ (name "r-delayedarray")
+ (version "0.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DelayedArray" version))
+ (sha256
+ (base32
+ "0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r"))))
+ (properties
+ `((upstream-name . "DelayedArray")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)))
+ (home-page "http://bioconductor.org/packages/DelayedArray")
+ (synopsis "Delayed operations on array-like objects")
+ (description
+ "Wrapping an array-like object (typically an on-disk object) in a
+@code{DelayedArray} object allows one to perform common array operations on it
+without loading the object in memory. In order to reduce memory usage and
+optimize performance, operations on the object are either delayed or executed
+using a block processing mechanism. Note that this also works on in-memory
+array-like objects like @code{DataFrame} objects (typically with Rle columns),
+@code{Matrix} objects, and ordinary arrays and data frames.")
+ (license license:artistic2.0)))
+
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.4.0")
+ (version "1.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "1kbj8sg2ik9f8d6g95wz0py62jldg01qy5rsdpg1cxw95nf7dzi3"))))
+ "1szjbzzz4pyip891nji71caalxh0rhqiv7rpv6q54swlrqpfkqkw"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
+ ("r-delayedarray" ,r-delayedarray)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.10.1")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "1dilghbsyf64iz5c0kib2c7if72x7almd5w3ali09a2b2ff2mcjk"))))
+ "1aagyrdk5309a7awg42lg0bpirp91i6i2ddvpmrs38pzriwahnjy"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.34.2")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "1j3cyvg1wg1d9l0lkcjk3jn7pb96zi17nd1qsa5lglsimja19mpl"))))
+ "0dv7p3wzmx57inznf6fb06417zcm48g7fpazyahxny7bqgzwq0ig"))))
(build-system r-build-system)
(arguments
`(#:phases
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.26.4")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "1y16lqach0v3ym5zhdhj4r2imfi0kpa0djlb51hj85yf7xkzwdlb"))))
+ "1pjxlr34ygv8pvfwpyq268wpgqzphiwpij85fyhjqdwdp0a253ik"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
(define-public r-graph
(package
(name "r-graph")
- (version "1.52.0")
+ (version "1.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "graph" version))
(sha256
(base32
- "0g3dk5vsdp489fmyg8mifczmzgqrjlakkkr8i96dj15gghp3l135"))))
+ "0hx9wslnrci7c5i1gd1zlpjmgrkdnx9gabfgmzzwfnykk1mdvvna"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
(define-public r-topgo
(package
(name "r-topgo")
- (version "2.26.0")
+ (version "2.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "topGO" version))
(sha256
(base32
- "0j6sgvam4lk9348ag6pypcbkv93x4fk0di8ivhr23mz2s2yqzwrx"))))
+ "04kvxz9qsxfz0np7wlrzp4r95nykz94x7mqpyyk76f90g6m66vcc"))))
(properties
`((upstream-name . "topGO")))
(build-system r-build-system)
(define-public r-bsgenome
(package
(name "r-bsgenome")
- (version "1.42.0")
+ (version "1.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome" version))
(sha256
(base32
- "0hxwc02h5mzhkrk60d1jmlsfjf0ai9jxdc0128kj1sg4r2k1q94y"))))
+ "18dlknwk3xvi52hamxf9pl5bjc5806mpw98xwvx5xajn8mrxiy5h"))))
(properties
`((upstream-name . "BSgenome")))
(build-system r-build-system)
(define-public r-impute
(package
(name "r-impute")
- (version "1.48.0")
+ (version "1.50.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "impute" version))
(sha256
(base32
- "1164zvnikbjd0ybdn9xwn520rlmdjd824vmhnl83zgv3v9lzp9bm"))))
+ "0va45vfixy3np549md87h3b3rbavm54gfnmnjhpr9hf02lll6zxs"))))
(inputs
`(("gfortran" ,gfortran)))
(build-system r-build-system)
(define-public r-seqpattern
(package
(name "r-seqpattern")
- (version "1.6.0")
+ (version "1.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "seqPattern" version))
(sha256
(base32
- "0lsa5pz36xapi3yiv78k3z286a5md5sm5g21pgfyg8zmhmkxr7y8"))))
+ "0yw5251sirv3283xgmfmfbf900xp8dwvqfk88mr945s3by5hx99v"))))
(properties
`((upstream-name . "seqPattern")))
(build-system r-build-system)
(define-public r-genomation
(package
(name "r-genomation")
- (version "1.6.0")
+ (version "1.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "genomation" version))
(sha256
(base32
- "1m4mz7wihj8yqivwkzw68div8ybk4rjsai3ffki7xp7sh21ax03y"))))
+ "0r71nf8p3aq3yffqxg4yir1zmm7rar5a57nmy1kpqpn8kaf2svjl"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
(define-public r-seqlogo
(package
(name "r-seqlogo")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "seqLogo" version))
(sha256
(base32
- "18bajdl75h3039559d81rgllqqvnq8ygsfxfx081xphxs0v6xggy"))))
+ "19d5zmy7m8svljwgbmrb4vxkq18slq0f3all6k2ayv42b8w44h6q"))))
(properties `((upstream-name . "seqLogo")))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/seqLogo")
(define-public r-motifrg
(package
(name "r-motifrg")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "motifRG" version))
(sha256
(base32
- "1pa97aj6c5f3gx4bgriw110764dj3m9h104ddi8rv2bpy41yd98d"))))
+ "0lxxpqyljiyk73vyq6ss46q13g81pm24q87mkzdsqlr5zx427ch6"))))
(properties `((upstream-name . "motifRG")))
(build-system r-build-system)
(propagated-inputs
(define-public r-zlibbioc
(package
(name "r-zlibbioc")
- (version "1.20.0")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "zlibbioc" version))
(sha256
(base32
- "0hbk90q5hl0fycfvy5nxxa4hxgglag9lzp7i0fg849bqygg5nbyq"))))
+ "1kdgwwlh39mgwzj3zq71za4iv40sq625ghnyrndv5wrivrcr2igv"))))
(properties
`((upstream-name . "zlibbioc")))
(build-system r-build-system)
(define-public r-rhtslib
(package
(name "r-rhtslib")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhtslib" version))
(sha256
(base32
- "1vk3ng61dhi3pbia1lp3gl3mlr3i1vb2lkq83qb53i9dzz128wh9"))))
+ "0jj5h81z5gyf4j3lp2l3zsm6pgbmalgrngr8qdpygc20phndpp0b"))))
(properties `((upstream-name . "Rhtslib")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bamsignals
(package
(name "r-bamsignals")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bamsignals" version))
(sha256
(base32
- "1k42gvk5mgq4la1fp0in3an2zfdz69h6522jsqhmk0f6i75kg4mb"))))
+ "0knx69zzdaak2sjim8k9mygmcjxpa705m8013ld5zwpgi8dag9mc"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
- (version "1.0.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
- "1a3c2bm0xx0q4gf98jiw74msmdf2fr8rbsdysd5ww9kqlzmsbr17"))))
+ "00jh1qklj8jb9j7mwvkfybq368h2wg9yc2cwkgb7yb9vsw72r61d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
+ ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
("r-genomicranges" ,r-genomicranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-ggplot2" ,r-ggplot2)
(define-public r-tximport
(package
(name "r-tximport")
- (version "1.2.0")
+ (version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "tximport" version))
(sha256
(base32
- "1k5a7dad6zqg936s17f6cmwgqp11x24z9zhxndsgwbscgpyhpcb0"))))
+ "1mklb02bj4gnbjlmb7vv6k4lr3w9fp3pzli9rddbrwd0y5n8fcpx"))))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/tximport")
(synopsis "Import and summarize transcript-level estimates for gene-level analysis")
(define-public r-rhdf5
(package
(name "r-rhdf5")
- (version "2.18.0")
+ (version "2.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5" version))
(sha256
(base32
- "0pb04li55ysag30s7rap7nnivc0rqmgsmpj43kin0rxdabfn1w0k"))))
+ "1p6f5i6l44phl772a38x9cav2sya37bkqbkjzdc4pmyfzkv1j6hy"))))
(build-system r-build-system)
(arguments
`(#:phases
(define-public r-chipseq
(package
(name "r-chipseq")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chipseq" version))
(sha256
(base32
- "115ayp82rs99iaswrx45skw1i5iacgwzz5k8rzijbp5qic0554n0"))))
+ "1hahyqiwb2ch8214xqpw0c3jpiwkmyf3dwz0xc87jx6cdnzipj3i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(define-public r-copywriter
(package
(name "r-copywriter")
- (version "2.6.0")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CopywriteR" version))
(sha256
(base32
- "1bwwnsyk7cpgwkagsnn5mv6fv233b0rkhjvbadrh70h8m4anawfj"))))
+ "183nmrqmdf9syqljslvwv7mhs9ar5xizzq98imgsc80q0m25ncjf"))))
(properties `((upstream-name . "CopywriteR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-sva
(package
(name "r-sva")
- (version "3.22.0")
+ (version "3.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sva" version))
(sha256
(base32
- "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
+ "04pxl61iyc845wmqca1qv8kbb8zcp0qp72zgvgki3zzmrph9a362"))))
(build-system r-build-system)
(propagated-inputs
`(("r-genefilter" ,r-genefilter)
(define-public r-seqminer
(package
(name "r-seqminer")
- (version "5.7")
+ (version "5.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqminer" version))
(sha256
(base32
- "0p75wyl70cvp36mwg5y74nv573j1gdqi15ac2a7xf61jmsq7ycpy"))))
+ "0sfkxrc9gy5a8fadzyzfzh7l5grasm8cj6cd2nnpv85ws6mqr6qd"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(define-public r-protgenerics
(package
(name "r-protgenerics")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ProtGenerics" version))
(sha256
(base32
- "0hb3vrrvfx6lcfalmjxm8dmigfmi5nba0pzjfgsrzd35c8mbfc6f"))))
+ "08idb3rvxn4fl7rd66jasyqz47cb76dbc3968r1g26jr2ci3w1pl"))))
(properties `((upstream-name . "ProtGenerics")))
(build-system r-build-system)
(home-page "https://github.com/lgatto/ProtGenerics")
(define-public r-mzr
(package
(name "r-mzr")
- (version "2.8.1")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzR" version))
(sha256
(base32
- "0ipmhg6l3pf648rdx5g2ha7l5ppd3cja6afxhdw76x8ga3633x0r"))))
+ "1zir46h320n2vbrky6q3m8l221f3wdjlfsnx4ak9xca5min24xm7"))))
(properties `((upstream-name . "mzR")))
(build-system r-build-system)
(inputs
(define-public r-affyio
(package
(name "r-affyio")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyio" version))
(sha256
(base32
- "1svsl4mpk06xm505pap913x69ywks99262krag8y4ygpllj7dfyy"))))
+ "13w6al9296q916w0w6ngbsk25b21ahla1b6n40fcqhbvhyfii6sj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-zlibbioc" ,r-zlibbioc)))
(define-public r-affy
(package
(name "r-affy")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affy" version))
(sha256
(base32
- "1snq71ligf0wvaxa6zfrl13ydw0zfhspmhdyfk8q3ba3np4cz344"))))
+ "0azwg2qxzgflr1rjvbdln5i5rbcr9gs36kqlacd9cwl1szb9ad3m"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affyio" ,r-affyio)
(define-public r-vsn
(package
(name "r-vsn")
- (version "3.42.3")
+ (version "3.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "vsn" version))
(sha256
(base32
- "0mgl0azys2g90simf8wx6jdwd7gyg3m4pf12n6w6507jixm2cg97"))))
+ "0qhg3a4sc62pfdxcpvmk831rk138xh4zx4f1s39jhxpqqhmr7jvk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
("r-biobase" ,r-biobase)
("r-ggplot2" ,r-ggplot2)
+ ("r-hexbin" ,r-hexbin)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)))
(home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html")
(define-public r-mzid
(package
(name "r-mzid")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzID" version))
(sha256
(base32
- "1zn896cpfvqp1qmq5c4vcj933hb8rxwb6gkck1wqvr7393rpqy1q"))))
+ "11xnild02jz24vbsfy92lb7jlqqwnrswg66a7r4rsw8d2ibrbk33"))))
(properties `((upstream-name . "mzID")))
(build-system r-build-system)
(propagated-inputs
(define-public r-pcamethods
(package
(name "r-pcamethods")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "pcaMethods" version))
(sha256
(base32
- "18mawhxw57pgpn87qha4mwki24gqja7wpqha8q496476vyap11xw"))))
+ "0c4lphqyzj577ws4s172391cgv00s5nhy152zp18k2k4diyhq6n0"))))
(properties `((upstream-name . "pcaMethods")))
(build-system r-build-system)
(propagated-inputs
(define-public r-msnbase
(package
(name "r-msnbase")
- (version "2.0.2")
+ (version "2.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnbase" version))
(sha256
(base32
- "0jjjs29dcwsjaxzfqxy98ycpg3rwxzzchkj77my3cjgdc00sm66n"))))
+ "1n9bbdlp8d8bx2mqby0c4yylz1yil42scbkxqgyrfr9s5sn6dqff"))))
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-msnid
(package
(name "r-msnid")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
- "0fkk3za39cxi0jyxmagmycjdslr2xf6vg3ylz14jyffqi0blw9d5"))))
+ "0pjwargi5lif8q53fd43ql67p3yk9w10jychafd9qgbaw5k3f68k"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs
HCoop / jackhill / guix / guix.git / blobdiff