ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
☆26Feb 3, 2022Updated 4 years ago
Alternatives and similar repositories for chipseq
Users that are interested in chipseq are comparing it to the libraries listed below
Sorting:
- ChIP-seq and ATAC-seq analysis☆13Jun 17, 2024Updated last year
- A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.☆68Feb 25, 2026Updated 3 weeks ago
- CRISPR Indel, base edit analysis☆11Aug 1, 2020Updated 5 years ago
- Develop custom oligo design pipelines.☆27Updated this week
- ☆13Apr 5, 2024Updated last year
- Variational Auto Encoders for learning binding signatures of transcription factors☆14Mar 14, 2024Updated 2 years ago
- Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.☆14Jun 6, 2024Updated last year
- An R package for detecting Gene-by-Environment (GxE) interaction effects on the transcriptome using Allele Specific Expression quantified…☆22Oct 27, 2021Updated 4 years ago
- CHANGE-seq analysis pipeline☆11Dec 18, 2025Updated 3 months ago
- Pipeline to call somatic cancer neoantigens from mutations in patient tumor DNA☆14Feb 16, 2023Updated 3 years ago
- ReMapEnrich is a R-software package to identify significantly enriched regions from ReMap catalogues or user defined catalogues. ReMapEnr…☆17Feb 2, 2022Updated 4 years ago
- Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed in…☆90Mar 6, 2024Updated 2 years ago
- RNAseq analysis in R workshop, originally taught: http://combine-australia.github.io/2016-05-11-RNAseq/☆24Dec 1, 2020Updated 5 years ago
- Common Snakemake rules and workflows mainly directed towards Metagenomic analysis.☆21Nov 15, 2018Updated 7 years ago
- Calculates the Variant Allele Fraction of variants in VCF files☆19Nov 28, 2024Updated last year
- Very large scale k-mer counting and analysis on Apache Spark.☆18Mar 2, 2026Updated 2 weeks ago
- Digenome-toolkit ver2.☆16Nov 1, 2021Updated 4 years ago
- Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C…☆11May 28, 2021Updated 4 years ago
- Tool for ribo-seq analysis. Most of the functionality moved to ribotricer (https://github.com/smithlabcode/ribotricer)☆13Mar 5, 2021Updated 5 years ago
- A tool that allows to get UMI counts from a single cell protein assay☆87Apr 23, 2025Updated 10 months ago
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆28Feb 21, 2023Updated 3 years ago
- Single Cell Consensus Clustering with Speed☆21Dec 12, 2022Updated 3 years ago
- Python script for calling SNPs, MNPs, and indels in mitochondrial DNA.☆10Apr 19, 2016Updated 9 years ago
- A pipeline for analyzing DNA methylation data from bisulfite sequencing.☆71Oct 7, 2022Updated 3 years ago
- This Snakemake pipeline implements the GATK best-practices workflow☆262Jun 8, 2023Updated 2 years ago
- A workflow for creating small NGS test data sets, useful for continuous integration.☆24Aug 15, 2024Updated last year
- Tool used to quantify extrachromosomal DNA (ecDNA) in metaphase images stained with DAPI and FISH probes.☆16Mar 3, 2026Updated 2 weeks ago
- Peak caller for CUT&TAG data☆30Aug 18, 2022Updated 3 years ago
- Scripts used for the ACT paper☆12May 6, 2021Updated 4 years ago
- R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework☆17Jan 7, 2025Updated last year
- Software to study why most genes are ignored☆15Sep 18, 2018Updated 7 years ago
- Base-conversion Sequencing Aligner☆14Nov 8, 2025Updated 4 months ago
- vembrane filters VCF records using python expressions☆69Updated this week
- GESTALT processing pipeline for barcodes captured with single-cell RNA sequencing☆13Jan 26, 2020Updated 6 years ago
- Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague☆14Aug 19, 2020Updated 5 years ago
- Tutorial for AMSI BioInfoSummer 2018☆29Dec 3, 2018Updated 7 years ago
- ☆20Jun 26, 2025Updated 8 months ago
- This is a repo that includes some resources about machine learning and the application in biology. We are students/alumni of Peking Unive…☆18Nov 10, 2019Updated 6 years ago
- Integrate multiple genome assemblies into a pangenome graph☆35Jun 9, 2022Updated 3 years ago