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environment_scRNAseq2021.yml
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environment_scRNAseq2021.yml
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## conda requirements for all packages needed to run the scanpy tutorials
# install with: mamba env create -n scRNAseq2021 -f environment.yml
# or with: conda env create -n scRNAseq2021 -f environment.yml
# then run: source activate scRNAseq2021
name: scRNAseq2021
channels:
- conda-forge
- anaconda
- bioconda
- defaults
- r
- rdonnelly
- psi4
- free
- fastchan
- ccordoba12
- grst
- Eugene_T
- letaylor
dependencies:
- r-base
- rstudio
- bioconductor-scater
- bioconductor-scran
- bioconductor-singlecellexperiment
- bioconductor-slingshot
- bioconductor-tradeseq
- bioconductor-destiny
- bioconductor-rhdf5
- bioconductor-fgsea
- bioconductor-biomart
- bioconductor-org.hs.eg.db
- bioconductor-scdblfinder
- bioconductor-biocsingular
- bioconductor-singler
- bioconductor-batchelor
- bioconductor-scmap
# - bioconductor-glmgampoi
# - bioconductor-scrnaseq
- r-scpred
- r-pheatmap
- r-harmony
- r-msigdbr
- r-rafalib
- r-enrichr
- r-devtools
- r-biocmanager
- r-dplyr
- r-igraph
- r-seurat>=3.1.2
- r-umap
- r-grr
- r-hdf5r
- r-bookdown
- r-venn
- r-uwot
- r-optparse
- r-fields
- r-ggraph
- r-checkmate
- r-tidygraph
- notebook
- jupyter_contrib_nbextensions
- nbconvert=5.6.1
- python-annoy
- multicore-tsne
- requests
- r-spam
- r-stringi
- wget
- compilers
- pip
- pip:
- annoy
- mnnpy
- scanpy
- scanorama
- numba
- python-igraph
- umap-learn==0.4.6
- louvain
- leidenalg
- matplotlib-venn
- scrublet
- gseapy
- gsea-api
- pybiomart
- scvelo
# Manual installation of packages that are not in conda:
# remotes::install_github('chris-mcginnis-ucsf/DoubletFinder', dependencies=FALSE)
# install.packages('clustree', dependencies=FALSE)
# remotes::install_github('satijalab/seurat-data', dependencies=FALSE)