Computational Epigenetics

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47 repositories

CellWhisperer
Public
CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets
Jupyter Notebook
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GNU General Public License v3.0
•13•139•2•0•Updated Nov 17, 2025Nov 17, 2025
MrBiomics
Public
MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses
python science recipes data-science automation bioinformatics snakemake framework r research
R
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MIT License
•1•127•26•0•Updated Nov 3, 2025Nov 3, 2025
cellxgene
Public
Fork of `cellxgene` repository with adaptations for CellWhisperer and SpotWhisperer
JavaScript
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MIT License
•1•0•1•1•Updated Oct 21, 2025Oct 21, 2025
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.
visualization workflow bioinformatics snakemake scrna-seq single-cell 10xgenomics biomedical-data-science cite-seq snrna-seq
R
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MIT License
•1•53•3•0•Updated Oct 20, 2025Oct 20, 2025
cemm.slurm.sm
Public
CeMM's Snakemake SLURM cluster profile
snakemake slurm cluster-profile
Python
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MIT License
•2•44•0•0•Updated Oct 8, 2025Oct 8, 2025
spilterlize_integrate
Public
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.
visualization workflow bioinformatics rna-seq snakemake integration pipeline ngs dimensionality-reduction chip-seq
R
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MIT License
•3•48•1•0•Updated Oct 2, 2025Oct 2, 2025
UCE
Public
UCE is a zero-shot foundation model for single-cell gene expression data
Python
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MIT License
•37•0•0•0•Updated Sep 29, 2025Sep 29, 2025
dea_limma
Public
A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.
visualization workflow bioinformatics rna-seq snakemake r statistics scrna-seq chip-seq atac-seq
R
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MIT License
•2•57•0•0•Updated Sep 25, 2025Sep 25, 2025
LLaVA
Public
This is a fork of the llava project with adaptations for CellWhisperer
Python
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Apache License 2.0
•0•0•0•0•Updated Sep 24, 2025Sep 24, 2025
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.
visualization workflow bioinformatics gene-sets rna-seq snakemake pipeline chip-seq atac-seq gene-set-enrichment
Python
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MIT License
•3•71•8•2•Updated Sep 24, 2025Sep 24, 2025
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.
visualization workflow data-science snakemake clustering heatmap data-visualization high-dimensional-data pca dimensionality-reduction
Python
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MIT License
•4•61•23•0•Updated Sep 12, 2025Sep 12, 2025
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.
visualization workflow bioinformatics snakemake scrna-seq single-cell biomedical-data-science perturbation-analysis snrna-seq sccrispr-seq
R
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MIT License
•2•51•2•0•Updated Sep 5, 2025Sep 5, 2025
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.
visualization workflow bioinformatics snakemake scrna-seq single-cell biomedical-data-science differential-expression-analysis volcano-plot snrna-seq
R
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MIT License
•11•51•3•0•Updated Sep 5, 2025Sep 5, 2025
atacseq_pipeline
Public
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
python bash workflow bioinformatics snakemake pipeline ngs atac-seq biomedical-data-science
Python
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MIT License
•2•93•3•0•Updated Sep 3, 2025Sep 3, 2025
ShinyCell2
Public
Fork of ShinyCell2 customised for SD/LDR HEACA Atlas.
R
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GNU General Public License v3.0
•9•0•0•0•Updated Aug 27, 2025Aug 27, 2025
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.
visualization python workflow bioinformatics rna-seq snakemake pipeline scrna-seq atac-seq genome-browser
Python
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MIT License
•1•53•2•0•Updated Aug 5, 2025Aug 5, 2025
rnaseq_pipeline
Public
RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
python bash workflow bioinformatics rna-seq snakemake pipeline ngs rnaseq biomedical-data-science
Python
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MIT License
•2•40•1•0•Updated Aug 5, 2025Aug 5, 2025
RnBeads
Public
Git working Repo synced to the Bioconductor: http://bioconductor.org/packages/devel/bioc/html/RnBeads.html
R
•14•8•26•1•Updated Jul 23, 2025Jul 23, 2025
macrophage-regulation
Public
Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation
bioinformatics rna-seq time-series systems-biology scrna-seq crispr immunology atac-seq transcriptomics epigenomics
Jupyter Notebook
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MIT License
•1•4•0•0•Updated Jul 20, 2025Jul 20, 2025
fetch_ngs
Public
Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.
database repository genomics ngs next-generation-sequencing bam fastq
Python
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MIT License
•0•40•1•0•Updated Jun 23, 2025Jun 23, 2025
RnBeads_web
Public
RnBeads website and online resources
HTML
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MIT License
•1•1•0•0•Updated Apr 10, 2025Apr 10, 2025
scEval
Public
Bock lab fork of scEval
Jupyter Notebook
•11•0•0•0•Updated Dec 28, 2024Dec 28, 2024
Geneformer
Public
Private fork of Geneformer
Python
•0•1•0•0•Updated Oct 3, 2024Oct 3, 2024
300BCG_analysis
Public
Jupyter Notebook
•1•2•1•0•Updated Jan 8, 2024Jan 8, 2024
300BCG_ATACseq_pipeline
Public
Jupyter Notebook
•0•0•0•0•Updated Jan 8, 2024Jan 8, 2024
scifiRNA-seq_publication
Public
The million-scale method for single-cell analysis
Jupyter Notebook
•0•10•2•4•Updated Jul 6, 2023Jul 6, 2023
LIQUORICE
Public
A tool to detect tissue- and cancer- specific epigenetic signatures in WGS data of liquid biopsies
Python
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GNU General Public License v3.0
•5•10•0•0•Updated Mar 30, 2023Mar 30, 2023
KPNN
Public
Knowledge-primed neural networks
Python
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GNU General Public License v3.0
•8•38•0•2•Updated Mar 24, 2023Mar 24, 2023
DNAmeth500species
Public
Comparative analysis of DNA methylation across more than 500 animal species
Jupyter Notebook
•4•6•1•0•Updated Oct 11, 2022Oct 11, 2022
open_pipelines
Public
Pipelines for NGS data preprocessing by the Bock lab and friends
bioinformatics rna-seq pipeline chip-seq atac-seq looper ngs-pipeline pypiper
Python
•11•22•9•3•Updated Aug 29, 2022Aug 29, 2022