rnaseq_new.yml

name: rnaseq
channels:
  - bioconda
  - anaconda
  - r
  - conda-forge
  - defaults
dependencies:
  ## confa-forge
  - conda-forge::python=3.7.6
  - conda-forge::r-base=3.5.1
  - conda-forge::r-optparse=1.6.6
  - conda-forge::r-gplots=3.0.1.1
  ## Preprocessing
  - bedops=2.4.39
  - gffread=0.9.12
  - fastqc=0.11.8
  ## Alignment & Quality
  - star=2.6.1d
  - hisat2=2.1.0
  - rseqc=3.0.0
  - preseq=2.0.3
  - samtools=1.9
  ## Duplications
  - picard=2.18.27
  - bioconductor-dupradar=1.12.1
  ## Expression
  - bioconductor-rsubread=1.32.4
  - subread=1.6.4
  - stringtie=1.3.5
  - bioconductor-edger=3.24.1
  - bioconductor-limma=3.38.3
  - csvtk=0.17.0
  ## Reports
  - multiqc=1.7
  - r-markdown=0.9
  - wkhtmltopdf=0.12.4