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Open Sustainable Technology

https://github.com/epigen/mr.pareto

MR. PARETO - Modules & Recipes for Pragmatic Augmentation of Research Efficiency Towards Optimum
automation bioinformatics biomedical data-science framework snakemake workflows
Added: over 1 year ago - Last Synced: 11 months ago - Created: March 28, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: /projects/review
  • Commits: 37
  • Committers: 2
  • Issues: 2
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 3
  • Forks: 0
  • Packages: 0
https://github.com/epigen/mixscape_seurat

A Snakemake workflow for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.
bioinformatics biomedical-data-science perturbation-analysis sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 14, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 20
  • Committers: 2
  • Issues: 4
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 2
  • Forks: 0
  • Packages: 0
https://github.com/epigen/dea_seurat

A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
bioinformatics biomedical-data-science differential-expression-analysis scrna-seq single-cell snakemake snrna-seq visualization volcano-plot workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 20, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 19
  • Committers: 2
  • Issues: 10
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 10
  • Forks: 10
  • Packages: 0
https://github.com/epigen/dea_limma

A Snakemake workflow for performing and visualizing differential expression analyses (DEA) on NGS data powered by the R package limma.
atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom r rna-seq scrna-seq snakemake statistics visualization volcano-plot workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: August 12, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 47
  • Committers: 3
  • Issues: 9
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 14
  • Forks: 0
  • Packages: 0
https://github.com/epigen/spilterlize_integrate

A Snakemake workflow to split, filter, normalize, integrate and select highly variable features of count matrices resulting from experiments with sequencing readout (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including diagnostic visualizations.
atac-seq batch-effect bioinformatics biomedical-data-science chip-seq count-matrix dimensionality-reduction integration ngs normalization pipeline rna-seq snakemake visualization workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: June 28, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 22
  • Committers: 2
  • Issues: 7
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 8
  • Forks: 0
  • Packages: 0