2. Create analysis environment

Conda

Conda environment.yml

name: r-4.4.1-env
channels:
  - tiledb
  - conda-forge
  - bioconda
  - r
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - _r-mutex=1.0.1=anacondar_1
  - _r-xgboost-mutex=2.0=cpu_0
  - _sysroot_linux-64_curr_repodata_hack=3=h69a702a_16
  - alsa-lib=1.2.12=h4ab18f5_0
  - aom=3.9.1=hac33072_0
  - argcomplete=3.5.2=pyhd8ed1ab_0
  - arpack=3.9.1=nompi_h77f6705_101
  - atk-1.0=2.38.0=h04ea711_2
  - attr=2.5.1=h166bdaf_1
  - aws-c-auth=0.7.22=hbd3ac97_10
  - aws-c-cal=0.7.1=h87b94db_1
  - aws-c-common=0.9.23=h4ab18f5_0
  - aws-c-compression=0.2.18=he027950_7
  - aws-c-event-stream=0.4.2=h7671281_15
  - aws-c-http=0.8.2=he17ee6b_6
  - aws-c-io=0.14.10=h826b7d6_1
  - aws-c-mqtt=0.10.4=hcd6a914_8
  - aws-c-s3=0.6.0=h365ddd8_2
  - aws-c-sdkutils=0.1.16=he027950_3
  - aws-checksums=0.1.18=he027950_7
  - aws-crt-cpp=0.27.3=hda66527_2
  - aws-sdk-cpp=1.11.329=h46c3b66_9
  - azure-core-cpp=1.13.0=h935415a_0
  - azure-identity-cpp=1.8.0=hd126650_2
  - azure-storage-blobs-cpp=12.12.0=hd2e3451_0
  - azure-storage-common-cpp=12.7.0=h10ac4d7_1
  - azure-storage-files-datalake-cpp=12.11.0=h325d260_1
  - binutils_impl_linux-64=2.40=ha1999f0_7
  - bioconductor-assorthead=1.0.0=r44hdfd78af_0
  - bioconductor-batchelor=1.22.0=r44he5774e6_0
  - bioconductor-beachmat=2.22.0=r44he5774e6_0
  - bioconductor-biobase=2.66.0=r44h3df3fcb_0
  - bioconductor-biocfilecache=2.14.0=r44hdfd78af_0
  - bioconductor-biocgenerics=0.52.0=r44hdfd78af_3
  - bioconductor-biocneighbors=2.0.0=r44he5774e6_0
  - bioconductor-biocparallel=1.40.0=r44he5774e6_1
  - bioconductor-biocsingular=1.22.0=r44he5774e6_0
  - bioconductor-bluster=1.16.0=r44he5774e6_0
  - bioconductor-cellid=1.14.0=r44he5774e6_0
  - bioconductor-data-packages=20250105.1=hdfd78af_0
  - bioconductor-delayedarray=0.32.0=r44h3df3fcb_1
  - bioconductor-delayedmatrixstats=1.28.0=r44hdfd78af_0
  - bioconductor-edger=4.4.0=r44h3df3fcb_0
  - bioconductor-fgsea=1.32.2=r44he5774e6_0
  - bioconductor-genomeinfodb=1.42.0=r44hdfd78af_2
  - bioconductor-genomeinfodbdata=1.2.13=r44hdfd78af_0
  - bioconductor-genomicranges=1.58.0=r44h3df3fcb_1
  - bioconductor-iranges=2.40.0=r44h3df3fcb_2
  - bioconductor-limma=3.62.1=r44h15a9599_1
  - bioconductor-m3drop=1.32.0=r44hdfd78af_0
  - bioconductor-matrixgenerics=1.18.0=r44hdfd78af_0
  - bioconductor-metapod=1.14.0=r44he5774e6_0
  - bioconductor-residualmatrix=1.16.0=r44hdfd78af_0
  - bioconductor-s4arrays=1.6.0=r44h3df3fcb_0
  - bioconductor-s4vectors=0.44.0=r44h3df3fcb_2
  - bioconductor-scaledmatrix=1.14.0=r44hdfd78af_0
  - bioconductor-scater=1.34.0=r44hdfd78af_0
  - bioconductor-scmerge=1.22.0=r44hdfd78af_0
  - bioconductor-scran=1.34.0=r44he5774e6_0
  - bioconductor-scuttle=1.16.0=r44he5774e6_0
  - bioconductor-singlecellexperiment=1.28.0=r44hdfd78af_0
  - bioconductor-sparsearray=1.6.0=r44h3df3fcb_0
  - bioconductor-sparsematrixstats=1.18.0=r44he5774e6_0
  - bioconductor-spatialexperiment=1.16.0=r44hdfd78af_0
  - bioconductor-summarizedexperiment=1.36.0=r44hdfd78af_0
  - bioconductor-ucsc.utils=1.2.0=r44h9ee0642_1
  - bioconductor-xvector=0.46.0=r44h15a9599_2
  - bioconductor-zlibbioc=1.52.0=r44h3df3fcb_2
  - blosc=1.21.6=hef167b5_0
  - brotli=1.1.0=hd590300_1
  - brotli-bin=1.1.0=hd590300_1
  - bwidget=1.9.14=ha770c72_1
  - bzip2=1.0.8=h4bc722e_7
  - c-ares=1.32.3=h4bc722e_0
  - ca-certificates=2025.1.31=hbcca054_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - cairo=1.18.0=hebfffa5_3
  - certifi=2025.1.31=pyhd8ed1ab_0
  - cfitsio=4.4.1=hf8ad068_0
  - clang-format=18.1.8=default_hf981a13_1
  - clang-format-18=18.1.8=default_hf981a13_1
  - clang-tools=18.1.8=default_hf981a13_1
  - click=8.1.7=unix_pyh707e725_0
  - contourpy=1.2.1=py312h8572e83_0
  - curl=8.12.1=h332b0f4_0
  - cycler=0.12.1=pyhd8ed1ab_0
  - cython=3.0.10=py312h30efb56_0
  - dav1d=1.2.1=hd590300_0
  - dbus=1.13.6=h5008d03_3
  - expat=2.6.4=h5888daf_0
  - fftw=3.3.10=nompi_hf1063bd_110
  - fmt=10.2.1=h00ab1b0_0
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=h77eed37_2
  - fontconfig=2.15.0=h7e30c49_1
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - fonttools=4.53.1=py312h41a817b_0
  - freetype=2.12.1=h267a509_2
  - freexl=2.0.0=h743c826_0
  - fribidi=1.0.10=h36c2ea0_0
  - gcc_impl_linux-64=14.1.0=h3c94d91_0
  - gdk-pixbuf=2.42.12=hb9ae30d_0
  - geos=3.12.2=he02047a_1
  - geotiff=1.7.3=hf7fa9e8_2
  - gettext=0.22.5=h59595ed_2
  - gettext-tools=0.22.5=h59595ed_2
  - gflags=2.2.2=he1b5a44_1004
  - gfortran_impl_linux-64=14.1.0=he4a1faa_0
  - ghostscript=10.03.1=h59595ed_0
  - giflib=5.2.2=hd590300_0
  - glib=2.80.3=h8a4344b_1
  - glib-tools=2.80.3=h73ef956_1
  - glog=0.7.1=hbabe93e_0
  - glpk=5.0=h445213a_0
  - gmp=6.3.0=hac33072_2
  - graphite2=1.3.13=h59595ed_1003
  - graphviz=11.0.0=hc68bbd7_0
  - gsl=2.7=he838d99_0
  - gst-plugins-base=1.24.7=h0a52356_0
  - gstreamer=1.24.7=hf3bb09a_0
  - gtk2=2.24.33=h6470451_5
  - gts=0.7.6=h977cf35_4
  - gxx_impl_linux-64=14.1.0=h2879b86_0
  - h5py=3.11.0=nompi_py312hb7ab980_102
  - harfbuzz=9.0.0=hda332d3_1
  - hdf4=4.2.15=h2a13503_7
  - hdf5=1.14.3=nompi_hdf9ad27_105
  - htslib=1.21=h5efdd21_0
  - icu=75.1=he02047a_0
  - igraph=0.10.13=hef0740d_0
  - imagemagick=7.1.1_36=pl5321h796dacf_0
  - jbig=2.1=h7f98852_2003
  - joblib=1.4.2=pyhd8ed1ab_0
  - jq=1.7.1=hd590300_0
  - json-c=0.17=h1220068_1
  - kaleido-core=0.2.1=h3644ca4_0
  - kealib=1.5.3=hee9dde6_1
  - kernel-headers_linux-64=3.10.0=h4a8ded7_16
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.5=py312h8572e83_1
  - krb5=1.21.3=h659f571_0
  - lame=3.100=h166bdaf_1003
  - lcms2=2.17=h717163a_0
  - ld_impl_linux-64=2.40=hf3520f5_7
  - leidenalg=0.10.2=py312h30efb56_0
  - lerc=4.0.0=h27087fc_0
  - libabseil=20240116.2=cxx17_he02047a_1
  - libaec=1.1.3=h59595ed_0
  - libarchive=3.7.4=hfca40fe_0
  - libarrow=17.0.0=h4b47046_3_cpu
  - libarrow-acero=17.0.0=he02047a_3_cpu
  - libarrow-dataset=17.0.0=he02047a_3_cpu
  - libarrow-substrait=17.0.0=hc9a23c6_3_cpu
  - libasprintf=0.22.5=h661eb56_2
  - libasprintf-devel=0.22.5=h661eb56_2
  - libavif16=1.1.0=h9b56c87_0
  - libblas=3.9.0=23_linux64_openblas
  - libbrotlicommon=1.1.0=hd590300_1
  - libbrotlidec=1.1.0=hd590300_1
  - libbrotlienc=1.1.0=hd590300_1
  - libcap=2.69=h0f662aa_0
  - libcblas=3.9.0=23_linux64_openblas
  - libclang-cpp15=15.0.7=default_h127d8a8_5
  - libclang-cpp18.1=18.1.8=default_hf981a13_1
  - libclang13=18.1.8=default_h9def88c_1
  - libcrc32c=1.1.2=h9c3ff4c_0
  - libcups=2.3.3=h4637d8d_4
  - libcurl=8.12.1=h332b0f4_0
  - libde265=1.0.15=h00ab1b0_0
  - libdeflate=1.21=h4bc722e_0
  - libdrm=2.4.124=hb9d3cd8_0
  - libedit=3.1.20191231=he28a2e2_2
  - libegl=1.7.0=ha4b6fd6_2
  - libev=4.33=hd590300_2
  - libevent=2.1.12=hf998b51_1
  - libexpat=2.6.4=h5888daf_0
  - libffi=3.4.2=h7f98852_5
  - libflac=1.4.3=h59595ed_0
  - libgcc=14.1.0=h77fa898_1
  - libgcc-devel_linux-64=14.1.0=h5d3d1c9_100
  - libgcc-ng=14.1.0=h69a702a_1
  - libgcrypt=1.11.0=h4ab18f5_1
  - libgd=2.3.3=h6f5c62b_11
  - libgdal=3.9.1=ha770c72_13
  - libgdal-core=3.9.1=hba09cee_13
  - libgdal-fits=3.9.1=hdd6600c_13
  - libgdal-grib=3.9.1=h5f34788_13
  - libgdal-hdf4=3.9.1=ha39a594_13
  - libgdal-hdf5=3.9.1=ha2ed5f0_13
  - libgdal-jp2openjpeg=3.9.1=h2ebfdf0_13
  - libgdal-kea=3.9.1=h2b45729_13
  - libgdal-netcdf=3.9.1=h94e7027_13
  - libgdal-pdf=3.9.1=h562c687_11
  - libgdal-pg=3.9.1=he047751_11
  - libgdal-postgisraster=3.9.1=he047751_11
  - libgdal-tiledb=3.9.1=hfcb00c0_8
  - libgdal-xls=3.9.1=h062f1c4_13
  - libgettextpo=0.22.5=h59595ed_2
  - libgettextpo-devel=0.22.5=h59595ed_2
  - libgfortran=3.0.0=1
  - libgfortran-ng=14.1.0=h69a702a_0
  - libgfortran5=14.1.0=hc5f4f2c_0
  - libgit2=1.8.1=he8d1d4c_1
  - libgl=1.7.0=ha4b6fd6_2
  - libglib=2.80.3=h8a4344b_1
  - libglu=9.0.3=h03adeef_0
  - libglvnd=1.7.0=ha4b6fd6_2
  - libglx=1.7.0=ha4b6fd6_2
  - libgomp=14.1.0=h77fa898_1
  - libgoogle-cloud=2.26.0=h26d7fe4_0
  - libgoogle-cloud-storage=2.26.0=ha262f82_0
  - libgpg-error=1.50=h4f305b6_0
  - libgrpc=1.62.2=h15f2491_0
  - libheif=1.17.6=gpl_hfa3466e_102
  - libhwloc=2.11.2=default_he43201b_1000
  - libiconv=1.17=hd590300_2
  - libjpeg-turbo=3.0.0=hd590300_1
  - libkml=1.3.0=hf539b9f_1021
  - liblapack=3.9.0=23_linux64_openblas
  - libleidenalg=0.11.1=h00ab1b0_0
  - libllvm14=14.0.6=hcd5def8_4
  - libllvm15=15.0.7=ha7bfdaf_5
  - libllvm18=18.1.8=h8b73ec9_1
  - liblzma=5.6.4=hb9d3cd8_0
  - libnetcdf=4.9.2=nompi_h135f659_114
  - libnghttp2=1.64.0=h161d5f1_0
  - libnsl=2.0.1=hd590300_0
  - libogg=1.3.5=h4ab18f5_0
  - libopenblas=0.3.27=pthreads_hac2b453_1
  - libopus=1.3.1=h7f98852_1
  - libparquet=17.0.0=h9e5060d_3_cpu
  - libpciaccess=0.18=hd590300_0
  - libpng=1.6.47=h943b412_0
  - libpq=16.4=h2d7952a_3
  - libprotobuf=4.25.3=h08a7969_0
  - libre2-11=2023.09.01=h5a48ba9_2
  - librsvg=2.58.2=h9564881_1
  - librttopo=1.1.0=hc670b87_16
  - libsanitizer=14.1.0=hcba0ae0_0
  - libsndfile=1.2.2=hc60ed4a_1
  - libspatialite=5.1.0=h15fa968_9
  - libsqlite=3.49.1=hee588c1_1
  - libssh2=1.11.1=hf672d98_0
  - libstdcxx=14.1.0=hc0a3c3a_1
  - libstdcxx-devel_linux-64=14.1.0=h5d3d1c9_100
  - libstdcxx-ng=14.1.0=h4852527_1
  - libsystemd0=255=h3516f8a_1
  - libthrift=0.19.0=hb90f79a_1
  - libtiff=4.7.0=h6565414_0
  - libtiledbsoma=1.12.3=h4074421_0
  - libudunits2=2.2.28=h40f5838_3
  - libunwind=1.7.2=he02047a_0
  - libutf8proc=2.8.0=h166bdaf_0
  - libuuid=2.38.1=h0b41bf4_0
  - libuv=1.48.0=hd590300_0
  - libvorbis=1.3.7=h9c3ff4c_0
  - libwebp=1.5.0=hae8dbeb_0
  - libwebp-base=1.5.0=h851e524_0
  - libxcb=1.17.0=h8a09558_0
  - libxcrypt=4.4.36=hd590300_1
  - libxgboost=2.1.3=cpu_h97e353d_3
  - libxkbcommon=1.7.0=h2c5496b_1
  - libxml2=2.13.5=h8d12d68_1
  - libzip=1.10.1=h2629f0a_3
  - libzlib=1.3.1=h4ab18f5_1
  - llvmlite=0.43.0=py312h9c5d478_0
  - lz4-c=1.9.4=hcb278e6_0
  - lzo=2.10=hd590300_1001
  - make=4.3=hd18ef5c_1
  - mathjax=2.7.7=ha770c72_3
  - matplotlib=3.9.1=py312h7900ff3_0
  - matplotlib-base=3.9.1=py312h9201f00_0
  - minizip=4.0.7=h401b404_0
  - mpfr=4.2.1=h38ae2d0_2
  - mpg123=1.32.6=h59595ed_0
  - munkres=1.1.4=pyh9f0ad1d_0
  - mysql-common=9.0.1=h266115a_4
  - mysql-libs=9.0.1=he0572af_4
  - ncurses=6.5=h59595ed_0
  - nspr=4.35=h27087fc_0
  - nss=3.105=hd34e28f_0
  - numba=0.60.0=py312h83e6fd3_0
  - oniguruma=6.9.10=hb9d3cd8_0
  - openjpeg=2.5.3=h5fbd93e_0
  - openssl=3.5.0=h7b32b05_0
  - orc=2.0.1=h17fec99_1
  - packaging=24.1=pyhd8ed1ab_0
  - pandoc=3.3=ha770c72_0
  - pango=1.54.0=h4c5309f_1
  - pcre2=10.44=h0f59acf_0
  - perl=5.32.1=7_hd590300_perl5
  - pillow=11.1.0=py312h80c1187_0
  - pip=24.0=pyhd8ed1ab_0
  - pixman=0.43.2=h59595ed_0
  - pkg-config=0.29.2=h4bc722e_1009
  - ply=3.11=pyhd8ed1ab_2
  - poppler=24.07.0=hb0d391f_0
  - poppler-data=0.4.12=hd8ed1ab_0
  - postgresql=16.4=hb2eb5c0_3
  - proj=9.4.1=h54d7996_1
  - pthread-stubs=0.4=h36c2ea0_1001
  - pulseaudio-client=17.0=hb77b528_0
  - pyparsing=3.1.2=pyhd8ed1ab_0
  - pyqt=5.15.9=py312h949fe66_5
  - pyqt5-sip=12.12.2=py312h30efb56_5
  - python=3.12.4=h194c7f8_0_cpython
  - python-dateutil=2.9.0=pyhd8ed1ab_0
  - python-igraph=0.11.6=py312h0e1f547_0
  - python-kaleido=0.2.1=pyhd8ed1ab_0
  - python_abi=3.12=4_cp312
  - pyyaml=6.0.2=py312h178313f_2
  - qhull=2020.2=h434a139_5
  - qt-main=5.15.8=h3155989_26
  - r-abind=1.4_5=r44hc72bb7e_1006
  - r-ape=5.8=r44hb424bfc_1
  - r-aricode=1.0.3=r44h0d4f4ea_1
  - r-arrow=17.0.0=r44he02047a_1
  - r-askpass=1.2.0=r44hb1dbf0f_1
  - r-assertthat=0.2.1=r44hc72bb7e_5
  - r-backports=1.5.0=r44hb1dbf0f_1
  - r-base=4.4.1=h518d376_15
  - r-base64enc=0.1_3=r44hb1dbf0f_1007
  - r-bbmle=1.0.25.1=r44hc72bb7e_1
  - r-bdsmatrix=1.3_7=r44h2b5f3a1_2
  - r-beeswarm=0.4.0=r44h2b5f3a1_4
  - r-bh=1.84.0_0=r44hc72bb7e_1
  - r-bibtex=0.5.1=r44hc72bb7e_2
  - r-bit=4.0.5=r44hb1dbf0f_2
  - r-bit64=4.0.5=r44hb1dbf0f_3
  - r-bitops=1.0_9=r44h2b5f3a1_0
  - r-blob=1.2.4=r44hc72bb7e_2
  - r-boot=1.3_30=r44hc72bb7e_2
  - r-broom=1.0.6=r44hc72bb7e_1
  - r-bslib=0.8.0=r44hc72bb7e_0
  - r-bwstest=0.2.3=r44h0d4f4ea_1
  - r-cachem=1.1.0=r44hb1dbf0f_1
  - r-cairo=1.6_2=r44h232ff4d_2
  - r-callr=3.7.6=r44hc72bb7e_1
  - r-catools=1.18.3=r44h93ab643_0
  - r-cellranger=1.1.0=r44hc72bb7e_1007
  - r-checkmate=2.3.2=r44hdb488b9_0
  - r-class=7.3_22=r44hb1dbf0f_2
  - r-classint=0.4_10=r44hc4980d5_1
  - r-cli=3.6.3=r44h0d4f4ea_1
  - r-clipr=0.8.0=r44hc72bb7e_3
  - r-cluster=2.1.6=r44hbcb9c34_1
  - r-codetools=0.2_20=r44hc72bb7e_1
  - r-colorspace=2.1_1=r44hdb488b9_0
  - r-colourvalues=0.3.9=r44h93ab643_2
  - r-commonmark=1.9.2=r44h2b5f3a1_0
  - r-conflicted=1.2.0=r44h785f33e_2
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  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdamage=1.1.6=hb9d3cd8_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.6=hb9d3cd8_0
  - xorg-libxfixes=6.0.1=hb9d3cd8_0
  - xorg-libxrender=0.9.11=hd590300_0
  - xorg-libxt=1.3.0=hd590300_1
  - xorg-libxxf86vm=1.1.6=hb9d3cd8_0
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - yq=3.4.3=pyhd8ed1ab_1
  - zlib=1.3.1=h4ab18f5_1
  - zstd=1.5.6=ha6fb4c9_0
  - pip:
      - aiobotocore==2.15.2
      - aiohappyeyeballs==2.4.4
      - aiohttp==3.11.9
      - aioitertools==0.12.0
      - aiosignal==1.3.1
      - annotated-types==0.7.0
      - asciitree==0.3.3
      - attrs==24.2.0
      - biocframe==0.5.11
      - biocutils==0.1.6
      - boto3==1.35.36
      - botocore==1.35.36
      - charset-normalizer==3.4.0
      - coloredlogs==15.0.1
      - fasteners==0.19
      - frozenlist==1.5.0
      - fsspec==2024.10.0
      - geniml==0.5.1
      - genomicranges==0.4.34
      - greenlet==3.1.1
      - gtars==0.0.15
      - humanfriendly==10.0
      - idna==3.10
      - iranges==0.2.12
      - jmespath==1.0.1
      - logmuse==0.2.8
      - markdown-it-py==3.0.0
      - mdurl==0.1.2
      - multidict==6.1.0
      - ncls==0.0.68
      - nlopt==2.9.0
      - numcodecs==0.14.1
      - numpy==1.26.4
      - pandas==2.2.3
      - pephubclient==0.4.5
      - peppy==0.40.7
      - polars==1.16.0
      - propcache==0.2.1
      - pyarrow==18.1.0
      - pybiocfilecache==0.4.0
      - pydantic==2.10.2
      - pydantic-core==2.27.1
      - pygments==2.18.0
      - pytz==2024.2
      - requests==2.32.3
      - rich==13.9.4
      - s3fs==2024.10.0
      - s3transfer==0.10.4
      - shellingham==1.5.4
      - sqlalchemy==2.0.36
      - typer==0.14.0
      - typing-extensions==4.12.2
      - tzdata==2024.2
      - ubiquerg==0.8.0
      - urllib3==2.2.3
      - wrapt==1.17.0
      - yarl==1.18.3
      - zarr==2.18.3
prefix: /project/.conda/envs/r-4.4.1-env

conda env create -f environment.yml