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v1.6.355567283 · ·
- MAMBA_ROOT_PREFIX now set to avoid user-defined conda installations - Updated python packages spatialdata-plot and spatialdata-plot - Fixed R package arrow installation for required codecs - Added R package msigdbdf for msigdbr - Fixed python pertpy installation - Added R package dsb for ADT normalization
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v1.6.02bbf98ef · ·
Python and R again in same environment. R is now 4.4.0. Installed and updated packages. - After separating R and python was not successfull, I went back to having python and R in the same conda environment. - Python and python packages are installed via conda if possible else pip. - R is not installed via conda (unreliable) but compiled within the conda environment. System dependencies are managed via conda however. - R packages are installed via the R package pak. System dependencies are managed again via conda. - R is now 4.4.0. All R packages were updated accordingly. - RStudio server and quarto were updated to the most recent version. - For spatial analysis, additional packages were installed (R: Voyager, VoltRon, Banksy, ..-; python: spatialdata, sopa, squidpy, ...).
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v1.5.0d2bbc97b · ·
- Updated R to version 4.3 - Updated all R CRAN, Bioconductor and github packages to their most recent versions - Switched to Seurat 5 for support of large datasets (using on-disk BPcells) and multimodal analyses (incl signac for scATAC-seq) - Updated quarto - Updated RStudio - Added bedtools and samtools