Installing cellAssign
Table of Contents
Introduction
cellAssign (Zhang et al. 2019) is a method that probabilistically assigns single cells to cell types based on known marker gene expression. Here, we automate installation of the package and all required dependencies.
conda environment specification
xargs -n100 conda create -y -n cellassign -c conda-forge -c bioconda <<EOF python=3.8 r-base=3.6 r-cellassign r-seurat r-spatstat=1.64 r-tensorflow=2.2.0 tensorflow-gpu=2.2.0 tensorflow-probability EOF
name: cellassign channels: - bioconda - conda-forge - defaults dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=1_gnu - _r-mutex=1.0.1=anacondar_1 - _tflow_select=2.1.0=gpu - absl-py=0.12.0=pyhd8ed1ab_0 - aiohttp=3.7.4=py38h497a2fe_0 - astor=0.8.1=pyh9f0ad1d_0 - astunparse=1.6.3=pyhd8ed1ab_0 - async-timeout=3.0.1=py_1000 - attrs=20.3.0=pyhd3deb0d_0 - binutils_impl_linux-64=2.35.1=h193b22a_2 - binutils_linux-64=2.35=h67ddf6f_30 - bioconductor-beachmat=2.2.0=r36he1b5a44_0 - bioconductor-biobase=2.46.0=r36h516909a_0 - bioconductor-biocgenerics=0.32.0=r36_0 - bioconductor-biocneighbors=1.4.0=r36he1b5a44_0 - bioconductor-biocparallel=1.20.0=r36he1b5a44_0 - bioconductor-biocsingular=1.2.0=r36he1b5a44_0 - bioconductor-delayedarray=0.12.0=r36h516909a_0 - bioconductor-delayedmatrixstats=1.8.0=r36_0 - bioconductor-edger=3.28.0=r36he1b5a44_0 - bioconductor-genomeinfodb=1.22.0=r36_0 - bioconductor-genomeinfodbdata=1.2.2=r36_0 - bioconductor-genomicranges=1.38.0=r36h516909a_0 - bioconductor-hdf5array=1.14.0=r36h516909a_0 - bioconductor-iranges=2.20.0=r36h516909a_0 - bioconductor-limma=3.42.0=r36h516909a_0 - bioconductor-rhdf5=2.30.0=r36he1b5a44_0 - bioconductor-rhdf5lib=1.8.0=r36h516909a_0 - bioconductor-s4vectors=0.24.0=r36h516909a_0 - bioconductor-scater=1.14.0=r36he1b5a44_0 - bioconductor-scran=1.14.1=r36he1b5a44_0 - bioconductor-singlecellexperiment=1.8.0=r36_0 - bioconductor-summarizedexperiment=1.16.0=r36_0 - bioconductor-xvector=0.26.0=r36h516909a_0 - bioconductor-zlibbioc=1.32.0=r36h516909a_0 - blinker=1.4=py_1 - brotlipy=0.7.0=py38h497a2fe_1001 - bwidget=1.9.14=ha770c72_0 - bzip2=1.0.8=h7f98852_4 - c-ares=1.17.1=h7f98852_1 - ca-certificates=2020.12.5=ha878542_0 - cachetools=4.2.1=pyhd8ed1ab_0 - cairo=1.16.0=h7979940_1007 - certifi=2020.12.5=py38h578d9bd_1 - cffi=1.14.5=py38ha65f79e_0 - chardet=4.0.0=py38h578d9bd_1 - click=7.1.2=pyh9f0ad1d_0 - cloudpickle=1.6.0=py_0 - colormath=3.0.0=py_2 - cryptography=3.4.6=py38ha5dfef3_0 - cudatoolkit=10.1.243=h036e899_8 - cudnn=7.6.5.32=hc0a50b0_1 - cupti=10.1.168=0 - 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xorg-libxdmcp=1.1.3=h7f98852_0 - xorg-libxext=1.3.4=h7f98852_1 - xorg-libxrender=0.9.10=h7f98852_1003 - xorg-renderproto=0.11.1=h7f98852_1002 - xorg-xextproto=7.3.0=h7f98852_1002 - xorg-xproto=7.0.31=h7f98852_1007 - xz=5.2.5=h516909a_1 - yarl=1.6.3=py38h497a2fe_1 - zipp=3.4.1=pyhd8ed1ab_0 - zlib=1.2.11=h516909a_1010 - zstd=1.4.9=ha95c52a_0 prefix: /scratch/midway2/aksarkar/miniconda3/envs/cellassign