environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
# use this to find packages: https://anaconda.org/
name: qbic-pipelines-rnadeseq-2.4
channels:
  - bioconda
  - conda-forge
  - defaults
  - r
dependencies:
  - bioconda::bioconductor-annotationdbi=1.62.2
  - bioconda::bioconductor-deseq2=1.40.2
  - bioconda::bioconductor-genefilter=1.82.1
  - bioconda::bioconductor-genomeinfodbdata=1.2.10
  - bioconda::bioconductor-impute=1.74.1
  - bioconda::bioconductor-limma=3.56.2
  - bioconda::bioconductor-pathview=1.40.0
  - bioconda::bioconductor-rtracklayer=1.60.0
  - bioconda::bioconductor-summarizedexperiment=1.30.2
  - bioconda::bioconductor-tximeta=1.18.0
  - bioconda::bioconductor-tximport=1.28.0
  - bioconda::bioconductor-vsn=3.68.0
  - conda-forge::pandoc=3.1.3
  - conda-forge::r-base=4.3.1
  - conda-forge::r-details=0.3.0
  - conda-forge::r-dplyr=1.1.2
  - conda-forge::r-dt=0.28
  - conda-forge::r-extrafont=0.19
  - conda-forge::r-formattable=0.2.1
  - conda-forge::r-ggplot2=3.4.2
  - conda-forge::r-ggrepel=0.9.3
  - conda-forge::r-ggvenn=0.1.10
  - conda-forge::r-gplots=3.1.3
  - conda-forge::r-gprofiler2=0.2.2
  - conda-forge::r-heatmaply=1.4.2
  - conda-forge::r-kableextra=1.3.4
  - conda-forge::r-knitr=1.43
  - conda-forge::r-optparse=1.7.3
  - conda-forge::r-pheatmap=1.0.12
  - conda-forge::r-plyr=1.8.8
  - conda-forge::r-rcolorbrewer=1.1_3
  - conda-forge::r-reshape2=1.4.4
  - conda-forge::r-rmarkdown=2.23
  - conda-forge::r-sessioninfo=1.2.2
  - conda-forge::r-svglite=2.1.1
  - conda-forge::r-tidyverse=2.0.0
  - conda-forge::r-yaml=2.3.7