channels:
  - pwwang  # r-ggradar, r-seuratwrappers
  - conda-forge
  - r
  - bioconda
  - nodefaults
  - pytorch  # for ClusTCR
  - svalkiers  # for ClusTCR
dependencies:
  - nodejs=22  # pipen-report
  - python=3.12
  - curl  # force using conda-forge version
  - pip
  - procps-ng
  - fontconfig
  - graphviz  # pipen-diagram
  - git  # for copier, used by pipen-report
  - uv
  - libiconv # fix git: error while loading shared libraries: libiconv.so.2
  - time  # for pipen-runinfo
  - wget
  - gcc_linux-64
  - r-base=4.4
  - pwwang::bioconductor-data-packages
  - bioconductor-fgsea
  - bioconductor-scater
  - bioconductor-glmgampoi
  - bioconductor-destiny  # ModuleScoreCalculator (diffusion map)
  - bioconda::bioconductor-deseq2
  - bioconda::bioconductor-edger
  - r-hdf5r  # Read_10x_h5() by Seurat
  - r-laplacesdemon  # TESSA
  - libgdal
  - r-logger
  - r-presto  # MarkersFinder
  - r-hash  # CDR3AAPhyschem
  - r-glmnet  # CDR3AAPhyschem
  # - r-matrixstats=1.1.0  # useNames = NA  deprecated
  - r-matrixstats  # useNames = NA  deprecated
  - r-broom.mixed  # CDR3AAPhyschem
  - r-seuratwrappers
  - r-harmony
  - r-future
  # needed by r-biopipen.utils
  - r-bracer
  - r-digest
  - r-doubletfinder
  - r-jsonlite
  - r-r6
  - r-seurat
  - r-systemfonts
  - r-testthat
  - r-tibble
  - r-tidyseurat
  - r-zip
  - bioconda::bioconductor-biocparallel
  - bioconda::bioconductor-celda
  - bioconda::bioconductor-mygene
  - bioconda::bioconductor-scdblfinder
  - pwwang::r-seuratdisk
  - r-qs2
  # Needed by r-scplotter
  - r-callr
  - r-seuratobject
  - pwwang::bioconductor-screpertoire=2.2
  - r-gridgraphics
  - r-metap
  - pwwang::r-tidyprompt
  ## Needed by r-plotthis
  - r-circlize
  # - r-ggplot2 > 4  # required by biopipen.utils.R
  - r-rlang
  - r-dplyr
  - r-tidyr
  - r-glue
  - r-forcats
  - r-gtable
  - r-reshape2
  - r-stringr
  - r-scales
  - r-gridtext
  - r-patchwork
  - r-ggrepel
  - r-ggnewscale
  - r-cowplot
  - r-zoo
  # Suggests
  - pwwang::r-sccatch
  - pwwang::r-sccdc
  - r-matrix
  - r-alluvial
  - bioconda::bioconductor-complexheatmap
  - r-cluster  # implictly required by bioconductor-complexheatmap
  - r-clustree
  - r-ggwordcloud
  - r-ggalluvial
  - r-ggvenndiagram
  - r-ggupset
  - r-ggpubr
  - r-ggforce
  - r-ggraph
  - r-ggridges
  - pwwang::bioconductor-ggmanh
  - r-qqplotr
  - r-hexbin
  - r-igraph
  - r-inext
  - r-scattermore
  - r-sf
  - r-terra
  - r-concaveman
  - r-plotroc
  - r-optimalcutpoints
  - r-proxyc
  - r-metr
  # Needed by r-enrichit
  - r-httr
  - bioconductor-qvalue
  # Needed by r-gglogger
  - r-cli
  - r-s7
  - faiss-cpu=1.13  # supports numpy v2
  - clustcr=2025  # adopted to work with numpy v2
  - mscorefonts  # additional fonts for plots
  - r-hitype  # sctype will also be supported
  - r-plotly
  - r-htmlwidgets
  # unable to load shared object: stringfish.so for the one from r channel
  - pwwang::r-stringfish
  - pip:
    - liana
    - celltypist2
    - biopython  # GIANA
    - scikit-learn  # GIANA
    - keras  # TESSA
    - tensorflow==2.20 # TESSA
    - umap-learn  # RunUMAP with umap.method = "umap-learn"
