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GitHub / qbic-pipelines / rnadeseq
Differential gene expression analysis and pathway analysis of RNAseq data
JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/qbic-pipelines%2Frnadeseq
Stars: 32
Forks: 20
Open Issues: 7
License: mit
Language: Nextflow
Repo Size: 62.4 MB
Dependencies:
53
Created: almost 5 years ago
Updated: 8 months ago
Last pushed: about 18 hours ago
Last synced: about 17 hours ago
Topics: deseq2, nextflow, pathway-analysis, pipeline, rnaseq
Files
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Readme
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Dependencies
environment.yml
conda
- bioconductor-deseq2 1.34.0.*
- bioconductor-genefilter 1.76.0.*
- bioconductor-genomeinfodbdata 1.2.7.*
- bioconductor-impute 1.68.0.*
- bioconductor-org.hs.eg.db 3.14.0.*
- bioconductor-org.mm.eg.db 3.14.0.*
- bioconductor-pathview 1.34.0.*
- bioconductor-rtracklayer 1.54.0.*
- bioconductor-summarizedexperiment 1.24.0.*
- bioconductor-tximeta 1.12.0.*
- bioconductor-tximport 1.22.0.*
- bioconductor-vsn 3.62.0.*
- pandoc 2.17.1.1.*
- r-base 4.1.2.*
- r-dplyr 1.0.9.*
- r-dt 0.20.*
- r-extrafont 0.17.*
- r-formattable 0.2.1.*
- r-ggplot2 3.3.5.*
- r-gplots 3.1.1.*
- r-gprofiler2 0.2.1.*
- r-kableextra 1.3.4.*
- r-knitr 1.37.*
- r-optparse 1.7.1.*
- r-pheatmap 1.0.12.*
- r-plyr 1.8.6.*
- r-reshape2 1.4.4.*
- r-rmarkdown 2.11.*
- r-svglite 2.1.0.*
- r-tidyverse 1.3.1.*
- r-yaml 2.2.2.*
- nf-core/tower-action v3 composite
.github/workflows/awstest.yml
actions
- nf-core/tower-action v3 composite
.github/workflows/branch.yml
actions
- mshick/add-pr-comment v1 composite
.github/workflows/ci.yml
actions
- Wandalen/wretry.action v1.0.11 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- actions/upload-artifact v2 composite
- nf-core/setup-nextflow v1 composite
- technote-space/get-diff-action v4 composite
- actions/checkout v3 composite
- actions/setup-node v3 composite
.github/workflows/linting.yml
actions
- actions/checkout v3 composite
- actions/setup-node v3 composite
- actions/setup-python v4 composite
- actions/upload-artifact v3 composite
- mshick/add-pr-comment v1 composite
- nf-core/setup-nextflow v1 composite
- psf/black stable composite
- dawidd6/action-download-artifact v2 composite
- marocchino/sticky-pull-request-comment v2 composite
- actions/checkout v2 composite
Dockerfile
docker
- condaforge/mambaforge latest build