change env, annot, & config export rules - Githubissues

epigen / MrBiomics

MrBiomics - Modules & Recipes augment Bioinformatics for Multi-Omics Analyses at Scale

MIT License

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change env, annot, & config export rules #19

Closed sreichl closed 1 month ago

sreichl commented 3 months ago

Consider changing env, annot, & config export rules so that they output

to {result_folder}/{module}/{envs|config}
instead of {result_folder}/{envs|config}

so that different runs are self-contained and easy to understand what annotation and config were used.

[x] think if this should be centralized and loaded from here (upside: only one maintenance point, downsides: external dependency, does not cover additional gene/feature lists)

commit message

git commit -m "move env, config, annot export into the result folder to be self-contained"

Modules

[x] Unsupervised Analysis
[x] Split, Filter, Normalize and Integrate Sequencing Data
[x] Differential Analysis Using limma
[x] Enrichment Analysis
[x] Genome Track Visualization
[x] scRNA-seq Processing using Seurat
[x] Differential Analysis using Seurat
[x] Perturbation Analysis using Mixscape from Seurat
[x] ATAC-seq Processing