diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 198 |
1 files changed, 118 insertions, 80 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10b70bab06..ecb60f2e24 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2370,14 +2370,14 @@ used visualizations.") (define-public r-dearseq (package (name "r-dearseq") - (version "1.8.1") + (version "1.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1")))) + "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -3279,14 +3279,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.38.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8")))) + "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -3566,13 +3566,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.64.0") + (version "2.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8")))) + "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -3698,13 +3698,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7")))) + "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3718,6 +3718,7 @@ analysis.") r-genomicranges r-genomicfeatures r-ggplot2 + r-ggvenndiagram r-gplots r-gtools r-dplyr @@ -3770,14 +3771,14 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.12.0") + (version "2.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65")))) + "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -4210,14 +4211,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.46.0") + (version "2.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b")))) + "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) @@ -4328,13 +4329,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.32.3") + (version "1.32.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "17nwcq2ivj3bdibdywfyjq4n6z0djispbh9ahqa55sp31ksq41xh")))) + "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -4388,13 +4389,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.48.3") + (version "1.48.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1")))) + "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -4692,13 +4693,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.52.2") + (version "3.52.4") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65")))) + "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -6568,13 +6569,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.6.3") + (version "1.6.5") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz")))) + (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -6805,14 +6806,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.6.1") + (version "3.6.4") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr")))) + "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -7667,14 +7668,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl")))) + "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs @@ -7693,14 +7694,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.20.0") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla")))) + "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs @@ -7725,14 +7726,14 @@ platform for merging tree with associated data and converting file formats.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.4.0") + (version "3.4.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4")))) + "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs @@ -8215,14 +8216,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4")))) + "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) @@ -9349,14 +9350,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.22.0") + (version "3.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp")))) + "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -9384,14 +9385,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02")))) + "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss")))) (build-system r-build-system) (propagated-inputs (list r-aplot @@ -9806,14 +9807,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.44.0") + (version "2.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4")))) + "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -11501,14 +11502,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.10.4") + (version "2.10.5") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "155h25gbagqns7wpriil17li0jkdd1z1pcz0dlnikdqj4saf97rl")))) + "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -11703,14 +11704,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.42.0") + (version "2.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m")))) + "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs @@ -11734,14 +11735,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359")))) + "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -11771,14 +11772,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.60.0") + (version "1.60.2") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f")))) + "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -11919,14 +11920,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.8.0") + (version "4.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj")))) + "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -11957,14 +11958,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.8.0") + (version "2.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y")))) + "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -12001,14 +12002,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr")))) + "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs @@ -13760,13 +13761,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc")))) + "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -13835,13 +13836,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.64.0") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126")))) + "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -14031,14 +14032,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h")))) + "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -14577,14 +14578,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.24.1") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday")))) + "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -14978,14 +14979,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.6.2") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn")))) + "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -15055,14 +15056,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w")))) + "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -15123,14 +15124,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv")))) + "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -15805,13 +15806,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq")))) + (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs @@ -16054,14 +16055,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh")))) + "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs @@ -16243,14 +16244,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh")))) + "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -16303,14 +16304,14 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6")))) + "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) @@ -16333,14 +16334,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni")))) + "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs @@ -16474,32 +16475,32 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj")))) + "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-complexheatmap - r-deseq2 r-dynamictreecut r-genie3 r-ggnetwork r-ggnewscale r-ggplot2 - r-ggpubr + r-ggrepel r-igraph r-intergraph r-matrixstats r-minet r-netrep r-networkd3 + r-patchwork r-rcolorbrewer r-reshape2 r-summarizedexperiment @@ -16742,6 +16743,43 @@ ensemble machine learning for the estimation of nuisance functions.") visualizing bisulfite sequencing data.") (license license:artistic2.0))) +(define-public r-dada2 + (package + (name "r-dada2") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "dada2" version)) + (sha256 + (base32 + "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x")))) + (properties `((upstream-name . "dada2"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-rcpp + r-rcppparallel + r-reshape2 + r-shortread + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://benjjneb.github.io/dada2/") + (synopsis + "Accurate, high-resolution sample inference from amplicon sequencing data") + (description + "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs) +from high-throughput amplicon sequencing data, replacing the coarser and less +accurate OTU clustering approach. The dada2 pipeline takes as input +demultiplexed fastq files, and outputs the sequence variants and their +sample-wise abundances after removing substitution and chimera errors. +Taxonomic classification is available via a native implementation of the RDP +naive Bayesian classifier, and species-level assignment to 16S rRNA gene +fragments by exact matching.") + (license license:lgpl2.0))) + (define-public r-dmrseq (package (name "r-dmrseq") @@ -17009,14 +17047,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl")))) + "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs |