environment.yaml

channels:
 - conda-forge
 - bioconda
 - defaults
dependencies:
 - r-base=3.5.1
 - rstudio=1.1.456
 - r-seurat=3.0.0 
 - bioconductor-biomart=2.38
 - r-biocmanager=1.30
 - r-pheatmap=1.0 
 - r-fields=9.6.1
 - r-optparse=1.6
 - r-umap=0.2
 - r-modes=0.7.0
 - umap-learn=0.3.8
 - wget
 - fftw=3.3.8
 - bioconductor-singlecellexperiment=1.4.0
 - bioconductor-scran=1.10.1
 - r-hdf5r=1.2.0
 - r-rmarkdown
 - r-knitr=1.20
 - r-mvoutlier=2.0.9
 - bioconductor-destiny=2.12.0
 - bioconductor-monocle=2.10.0
 - r-umap=0.2.0.0
 - bioconductor-scnorm=1.4.3
 - bioconductor-hsmmsinglecell=1.2.0
 - bioconductor-netbiov=1.16.0
 - bioconductor-scde=2.10.0
 - bioconductor-mast=1.8.1
 - bioconductor-sc3=1.10.0
 - r-sctransform=0.2.0
 - r-outliers=0.14
 - bioconductor-gseabase=1.44.0
 - bioconductor-gsva=1.30.0
 - r-dofuture=0.8.0
 - bioconductor-singscore=1.2.2
 - clang=4.0.1
 - gcc=4.8.5
 - r-flexmix=2.3_15
 # for CHETAH
 - bioconductor-biodist=1.54.0
 - r-dendextend=1.10.0
 - r-cowplot=0.9.4
 - r-corrplot=0.84




# pbmcapply - has no conda, but cran.
# singleR - is devtools installation