So, as discussed, this will be the first PR to incorporate changes made in prerelease1_andpet into master. I will then continue using this branch for further development towards release. The content of the PR is:
Possiblity to use reciprocal pca for integration
Updated the cell/feature filter tables so that they look better
Added an script for running scrnaseq_hto.Rmd non-interactively
Added possiblity to downsample cells for DEG testing for speed
Added script for applying the per-sample results of the scrnaseq_hto workflow to the aggregated result generated by cellranger.
Added lists, colours, marker and degs to the Seurat object as well as some metadata
Export to anndata for cellxgene
Added additional output: Counts with metadata as sparse assay, cell metadata and gene annotation as Excel table
andpet0101
commented
3 years ago
So, as discussed, this will be the first PR to incorporate changes made in prerelease1_andpet into master. I will then continue using this branch for further development towards release. The content of the PR is:
Closes #71, closes #13, closes #66, closes #77, closes #81, closes #80, closes #74, closes #61.
Many changes are up for discussion. I tried to follow the style guide but the major focus here should be on code and functionality.
Have fun!