environment.yaml

name: somatic_n-of-1
channels:
  - bioconda
  - conda-forge
  - r
  - pcgr
dependencies:
  - ascat
  - bam-readcount
  - bbmap
  - bcftools
  - bedtools
  - bioconductor-biomart
  - bioconductor-bsgenome
  - bioconductor-bsgenome.hsapiens.ucsc.hg19
  - bioconductor-bsgenome.hsapiens.ucsc.hg38
  - bioconductor-complexheatmap
  - bioconductor-customprodb
  - bioconductor-dnacopy
  - bioconductor-ensdb.hsapiens.v75
  - bioconductor-ensdb.hsapiens.v86
  - bioconductor-ensembldb
  - bioconductor-ensemblvep
  - bioconductor-genomeinfodb
  - bioconductor-genomicalignments
  - bioconductor-genomicfeatures
  - bioconductor-genomicranges
  - bioconductor-mutationalpatterns
  - bioconductor-org.hs.eg.db
  - bioconductor-purecn
  - bioconductor-summarizedexperiment
  - bioconductor-structuralvariantannotation
  - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene
  - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
  - bioconductor-variantannotation
  - bwa
  - bzip2
  - cairo
  - ensembl-vep
  - fastp
  - fastqc
  - gatk4
  - htslib
  - markdown
  - mosdepth
  - multiqc
  - octopus
  - p7zip
  - pcre
  - perl
  - picard
  - pisces
  - r-base=3.6.2
  - r-bedr
  - r-biocmanager
  - r-circlize
  - r-dbplyr
  - r-deconstructsigs
  - r-devtools
  - r-dt
  - r-facets
  - r-forcats
  - r-ggrepel
  - r-ggsignif
  - r-httr
  - r-kernlab
  - r-kernsmooth
  - r-lubridate
  - r-magrittr
  - r-nlme
  - r-nmf
  - r-openssl
  - r-openxlsx
  - r-pctgcdata
  - r-pheatmap
  - r-plyr
  - r-rcpp
  - r-reactable
  - r-readxl
  - r-reshape2
  - r-rmarkdown
  - r-rpart
  - r-shiny
  - r-stringi
  - r-stringr
  - r-survival
  - r-testthat
  - r-tibble
  - r-tidyr
  - r-tidyselect
  - r-tidyverse
  - r-tinytex
  - r-xtable
  - samtools
  - snp-pileup
  - tabix
  - ucsc-liftover
  - unzip
  - varlociraptor
  - varscan
  - vcf2maf
  - vcfanno
  - vt
  - wget
prefix: /opt/miniconda/envs/somatic_n-of-1