MACS -- Model-based Analysis of ChIP-Seq
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Feb 21, 2025 - Python
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atac-seq
Here are 51 public repositories matching this topic...
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
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Jan 24, 2025 - Python
ATAC-seq and DNase-seq processing pipeline
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Jun 21, 2022 - 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
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
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
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Dec 20, 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
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
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Feb 28, 2025 - Python
A Python package for fast operations on 1-dimensional genomic signal tracks
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Apr 3, 2020 - Python
A toolkit for working with ATAC-seq data.
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Jun 11, 2024 - Python
Pipelines for NGS data preprocessing by the Bock lab and friends
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Aug 29, 2022 - Python
Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).
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Feb 12, 2025 - Python
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 genomic-regions biomedical-data-science genome-track
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Dec 20, 2024 - 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
Coupled clustering of single cell genomic data
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Sep 21, 2021 - Python
Variational Auto Encoders for learning binding signatures of transcription factors
machine-learning deep-learning tensorflow dna vae atac-seq motif-discovery transcription-factor variational-auto-encoder dna-sequence
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Mar 14, 2024 - Python
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