Computational Epigenetics

All

42 repositories

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
•2•32•2•1•Updated Dec 19, 2024Dec 19, 2024
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•26•28•5•Updated Dec 18, 2024Dec 18, 2024
MrBiomics
Public
MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses
python science recipes data-science automation bioinformatics snakemake framework r research
Python
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MIT License
•1•41•18•0•Updated Dec 16, 2024Dec 16, 2024
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•24•6•0•Updated Dec 3, 2024Dec 3, 2024
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•16•2•0•Updated Dec 3, 2024Dec 3, 2024
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•48•4•0•Updated Nov 21, 2024Nov 21, 2024
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•18•3•0•Updated Nov 19, 2024Nov 19, 2024
cemm.slurm.sm
Public
CeMM's Snakemake SLURM cluster profile
snakemake slurm cluster-profile
Shell
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MIT License
•1•13•0•0•Updated Nov 13, 2024Nov 13, 2024
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.
visualization workflow bioinformatics rna-seq snakemake integration pipeline ngs dimensionality-reduction chip-seq
Python
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MIT License
•3•14•6•1•Updated Nov 12, 2024Nov 12, 2024
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
•1•14•1•0•Updated Nov 6, 2024Nov 6, 2024
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•19•2•0•Updated Nov 6, 2024Nov 6, 2024
RnBeads
Public
Git working Repo synced to the Bioconductor: http://bioconductor.org/packages/devel/bioc/html/RnBeads.html
R
•11•7•21•0•Updated Nov 5, 2024Nov 5, 2024
cellxgene
Public
Bare clone of cellxgene
JavaScript
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MIT License
•0•0•0•1•Updated Oct 28, 2024Oct 28, 2024
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
•7•45•2•0•Updated Oct 18, 2024Oct 18, 2024
Geneformer
Public
Private fork of Geneformer
Python
•0•1•0•0•Updated Oct 3, 2024Oct 3, 2024
LLaVA
Public
Python
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Apache License 2.0
•0•0•0•0•Updated Oct 1, 2024Oct 1, 2024
rnaseq_pipeline
Public
RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module..
Python
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MIT License
•205•4•1•0•Updated Sep 15, 2024Sep 15, 2024
RnBeads_web
Public
RnBeads website and online resources
HTML
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MIT License
•0•1•0•0•Updated May 15, 2024May 15, 2024
300BCG_analysis
Public
Jupyter Notebook
•1•1•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•9•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•34•0•2•Updated Mar 24, 2023Mar 24, 2023
DNAmeth500species
Public
Comparative analysis of DNA methylation across more than 500 animal species
Jupyter Notebook
•3•5•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 chip-seq atac-seq looper ngs-pipeline pypiper pipeline
Python
•11•20•9•3•Updated Aug 29, 2022Aug 29, 2022
RnBeadsAnnotationCreator
Public
R
•2•0•1•0•Updated Jun 22, 2022Jun 22, 2022
scifiRNA-seq
Public
Python
•
GNU General Public License v3.0
•5•12•7•0•Updated Dec 7, 2020Dec 7, 2020
microtest
Public
Small test data from various data types for testing pipelines
bioinformatics test-data
Shell
•3•1•2•0•Updated Oct 7, 2020Oct 7, 2020
base-editor-design-tool
Public
This tool designs guides for use with the base editor technology.
Python
•8•0•0•0•Updated Apr 22, 2020Apr 22, 2020
Artemether_scRNA
Public
Single cell RNA-seq analysis of pancreatic islets with drug treatment
R
•0•4•0•0•Updated Mar 25, 2020Mar 25, 2020