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GitHub / dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dib-lab%2Felvers

Stars: 28
Forks: 3
Open Issues: 63

License: other
Language: Python
Repo Size: 106 MB
Dependencies: 134

Created: almost 6 years ago
Updated: 10 months ago
Last pushed: over 3 years ago
Last synced: 5 months ago

Topics: bioinformatics, rnaseq-analysis, transcriptomics

Files

Readme

Dependencies

elvers/rules/bowtie2/environment.yml conda

bowtie2 2.3.2.*
samtools 1.5.*

elvers/rules/dammit/environment.yml conda

dammit 1.2.*

elvers/rules/deseq2/environment.yml conda

elvers/rules/edgeR/environment.yml conda

bioconductor-annotate 1.56.0.*
bioconductor-annotationdbi 1.40.0.*
bioconductor-biobase 2.38.0.*
bioconductor-biocgenerics 0.24.0.*
bioconductor-biocparallel 1.12.0.*
bioconductor-delayedarray 0.4.1.*
bioconductor-edger 3.20.7.*
bioconductor-genefilter 1.60.0.*
bioconductor-geneplotter 1.56.0.*
bioconductor-genomeinfodb 1.14.0.*
bioconductor-genomeinfodbdata 1.0.0.*
bioconductor-genomicranges 1.30.0.*
bioconductor-iranges 2.12.0.*
bioconductor-s4vectors 0.16.0.*
bioconductor-summarizedexperiment 1.8.0.*
bioconductor-tximport 1.6.0.*
bioconductor-xvector 0.18.0.*
bioconductor-zlibbioc 1.24.0.*
r-acepack 1.4.1.*
r-backports 1.0.5.*
r-base 3.4.1.*
r-base64enc 0.1_3.*
r-bh 1.65.0_1.*
r-bit 1.1_12.*
r-bit64 0.9_5.*
r-bitops 1.0_6.*
r-blob 1.1.0.*
r-catools 1.17.1.*
r-checkmate 1.8.2.*
r-cluster 2.0.6.*
r-colorspace 1.3_2.*
r-dbi 0.6_1.*
r-dichromat 2.0_0.*
r-digest 0.6.12.*
r-evaluate 0.10.*
r-foreign 0.8_67.*
r-formula 1.2_1.*
r-futile.logger 1.4.3.*
r-futile.options 1.0.0.*
r-gdata 2.17.0.*
r-getopt 1.20.0.*
r-ggplot2 2.2.0.*
r-gplots 3.0.1.*
r-gridextra 2.2.1.*
r-gtable 0.2.0.*
r-gtools 3.5.0.*
r-highr 0.6.*
r-hmisc 4.0_3.*
r-htmltable 1.9.*
r-htmltools 0.3.6.*
r-htmlwidgets 0.9.*
r-jsonlite 1.4.*
r-kernsmooth 2.23_15.*
r-knitr 1.16.*
r-labeling 0.3.*
r-lambda.r 1.1.9.*
r-lattice 0.20_34.*
r-latticeextra 0.6_28.*
r-lazyeval 0.2.0.*
r-locfit 1.5_9.1.*
r-magrittr 1.5.*
r-markdown 0.8.*
r-mass 7.3_45.*
r-matrix 1.2_7.1.*
r-matrixstats 0.52.2.*
r-memoise 1.1.0.*
r-mime 0.5.*
r-munsell 0.4.3.*
r-nnet 7.3_12.*
r-pkgconfig 2.0.1.*
r-plogr 0.1_1.*
r-plyr 1.8.4.*
r-rcolorbrewer 1.1_2.*
r-rcpp 0.12.13.*
r-rcpparmadillo 0.7.800.2.0.*
r-rcurl 1.95_4.8.*
r-reshape2 1.4.2.*
r-rjson 0.2.15.*
r-rlang 0.1.2.*
r-rpart 4.1_10.*
r-rsqlite 2.0.*
r-scales 0.4.1.*
r-snow 0.4_2.*
r-stringi 1.1.2.*
r-stringr 1.2.0.*
r-survival 2.40_1.*
r-tibble 1.3.3.*
r-viridis 0.4.0.*
r-viridislite 0.2.0.*
r-xml 3.98_1.6.*
r-xtable 1.8_2.*
r-yaml 2.1.14.*

elvers/rules/fastqc/environment.yml conda

fastqc 0.11.8.*

elvers/rules/khmer/environment.yml conda

khmer 2.1.2.*

elvers/rules/multiqc/environment.yml conda

multiqc 1.7.*

elvers/rules/paladin/environment.yml conda

paladin 1.4.4.*
samtools 1.5.*

elvers/rules/pear/environment.yml conda

pear 0.9.6.*

elvers/rules/plass/environment.yml conda

plass 3.764a3.*

elvers/rules/rcorrector/environment.yml conda

rcorrector 1.0.3.*

elvers/rules/salmon/environment.yml conda

salmon 1.1.0.*

elvers/rules/sourmash/environment.yml conda

sourmash

elvers/rules/trimmomatic/environment.yml conda

pigz 2.3.4.*
trimmomatic 0.38.*

elvers/rules/trinity/environment.yml conda

trinity 2.11.*

environment.yml conda

requirements.txt pypi