ChIP-seq analysis notes from Ming Tang
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Aug 5, 2024 - Python
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chip-seq
Here are 65 public repositories matching this topic...
MACS -- Model-based Analysis of ChIP-Seq
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Nov 30, 2024 - Python
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
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
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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Jan 31, 2025 - Python
(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
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Nov 21, 2018 - Python
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
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Oct 18, 2024 - Python
A Python package for fast operations on 1-dimensional genomic signal tracks
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Apr 3, 2020 - Python
A robust model for quantitative comparison of ChIP-Seq data sets.
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May 18, 2020 - Python
Pipelines for NGS data preprocessing by the Bock lab and friends
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Aug 29, 2022 - Python
A toolkit for NGS analysis with Python
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Jan 18, 2023 - Python
The ChIP-Seq peak calling algorithm using convolution neural networks
bioinformatics tensorflow gpu docker-image chip-seq atac-seq nvidia-docker convolutional-neural-network samtools cnn-model ngs-analysis peak-calling progressbar2
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Jan 18, 2021 - Python
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 atac-seq normalization biomedical-data-science batch-effect count-matrix
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Dec 20, 2024 - Python
Pipeline to analyse ChIP-Rx data, i.e ChIP-Seq with reference exogenous genome spike-in normalization
bioinformatics snakemake bioinformatics-pipeline chip-seq snakemake-workflows normalisation spike-ins
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Jan 24, 2025 - Python
To pre-process a set of ChIP-seq samples and coordinate with MAnorm2 for differential analysis
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Apr 2, 2019 - Python
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