update documentation - Githubissues

epigen / scrnaseq_processing_seurat

A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

https://epigen.github.io/scrnaseq_processing_seurat/

MIT License

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update documentation #19

Closed sreichl closed 9 months ago

sreichl commented 9 months ago

[x] update current docs (work through current README)
[x] incorporate changes to latest features
- [x] restructuring of results and plots
[x] add latest features
- [x] heatmaps: rows are clustered and cells downsampled
- [x] pseudobulking
- [x] extended gRNA & KO call assignment
- [x] sctransform flavor v2
- [x] tested on 3 datasets of different sizes (10k-350k cells) and all modalities (RNA, Antibody, CRISPR, Custom)
[x] generalize config.yaml