ChIP-seq analysis notes from Ming Tang
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Aug 5, 2024 - Python
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chip-seq
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MACS -- Model-based Analysis of ChIP-Seq
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Nov 30, 2024 - Python
A collection of Galaxy-related training material
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Dec 24, 2024 - HTML
🎯 ChIP peak Annotation, Comparison and Visualization
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Oct 30, 2024 - R
ChIP-seq peak-calling, QC and differential analysis pipeline.
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Dec 24, 2024 - Nextflow
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
bioinformatics rna-seq snakemake pipeline reproducible-research ngs bioinformatics-pipeline chip-seq atac-seq workflows fastq sra
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Feb 5, 2024 - Python
Publication quality NGS track plotting
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Jun 27, 2022 - Python
AQUAS TF and histone ChIP-seq pipeline
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Jun 21, 2022 - Java
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
bioinformatics dnase-seq genomics ngs motif chip-seq atac-seq motif-analysis footprinting differential-peak-calling
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Nov 16, 2024 - Python
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
workflow rna-seq pipeline nextflow shiny deseq2 microarray chip-seq atac-seq differential-expression limma gsea nf-core differential-abundance
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Dec 24, 2024 - Nextflow
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
tfs roadmap gene rna-seq motif gene-expression regulation epigenetics encode cell chip-seq hotspot plasticity transcription-factor-binding motifs epigenomics fimo haystack-bio specific-regions haystack-pipeline
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Jun 21, 2022 - HTML
Go / Golang Bioinformatics Library
golang coverage bam-files bioinformatics bigwig chip-seq golang-library gtf bigwig-files bioinformatics-containers genomic-ranges
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Oct 13, 2024 - Go
deepStats: a stastitical toolbox for deeptools and genomic signals
bootstrap dnase-seq rna-seq dataviz genomics sequencing statistical-analysis chip-seq atac-seq galaxy vizualize-data genomics-visualization mnase-seq deeptools genomic-signals
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Jul 5, 2021 - R
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 enrichment-analysis genomic-regions biomedical-data-science motif-enrichment-analysis
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Dec 20, 2024 - Python
MAnorm2 for Normalizing and Comparing ChIP-seq Samples
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Nov 3, 2022 - HTML
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