Computational Epigenetics
- 29 followers
- Vienna, Austria
- http://www.medical-epigenomics.org/
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Repositories
- spilterlize_integrate Public
A Snakemake workflow and MrBiomics module 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.
epigen/spilterlize_integrate’s past year of commit activity - enrichment_analysis Public
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
epigen/enrichment_analysis’s past year of commit activity - mixscape_seurat Public
A Snakemake workflow and MrBiomics module 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.
epigen/mixscape_seurat’s past year of commit activity - dea_seurat Public
A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
epigen/dea_seurat’s past year of commit activity - scrnaseq_processing_seurat Public
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.
epigen/scrnaseq_processing_seurat’s past year of commit activity - atacseq_pipeline Public
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
epigen/atacseq_pipeline’s past year of commit activity - genome_tracks Public
A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.
epigen/genome_tracks’s past year of commit activity - unsupervised_analysis Public
A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.
epigen/unsupervised_analysis’s past year of commit activity
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