Analysis pipeline for ATAC-seq data
☆87Oct 30, 2023Updated 2 years ago
Alternatives and similar repositories for ATAC-seq
Users that are interested in ATAC-seq are comparing it to the libraries listed below
Sorting:
- Basic workflow for ATAC-seq analysis☆94Feb 23, 2024Updated 2 years ago
- Code associated with with the 2023 Nature Genetics Paper "Region Capture Micro-C reveals coalescence of enhancers and promoters into nest…☆12May 31, 2023Updated 2 years ago
- ☆145Jan 7, 2019Updated 7 years ago
- ENCODE ATAC-seq pipeline☆448Jul 18, 2024Updated last year
- ☆30Sep 22, 2023Updated 2 years ago
- Tutorial Website☆65Feb 1, 2021Updated 5 years ago
- A Shiny web app for mapping datasets using Seurat v4☆145Nov 5, 2024Updated last year
- scRNA analysis of public dataset on bladder cancer☆19Dec 12, 2025Updated 3 months ago
- Reproducibility repository for the Human Neural Organoid Atlas publication☆43Dec 16, 2024Updated last year
- Website Deployment for CRC User Manual☆12Jan 15, 2026Updated 2 months ago
- Step-by-step analysis pipeline for RNA-seq data☆165Sep 5, 2023Updated 2 years ago
- Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis☆74Apr 22, 2024Updated last year
- Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal☆241Updated this week
- ☆32Oct 4, 2024Updated last year
- R code in workflow of chip-seq analysis☆11Nov 20, 2019Updated 6 years ago
- Genomic coordinates of problematic genomic regions as GRanges☆51Dec 10, 2025Updated 3 months ago
- Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".☆132Sep 6, 2024Updated last year
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆246Jan 16, 2026Updated 2 months ago
- ☆60Feb 9, 2026Updated last month
- Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)☆32Feb 22, 2018Updated 8 years ago
- Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling …☆14Dec 22, 2025Updated 2 months ago
- De novo construction of isoforms from long-read data☆35Jun 10, 2025Updated 9 months ago
- Whole mouse brain snATAC seq analysis☆29Apr 18, 2025Updated 11 months ago
- Blazing fast toolkit to work with .hic and .cool files☆42Updated this week
- ☆26Apr 1, 2025Updated 11 months ago
- ☆17Updated this week
- AUCell: score single cells with gene regulatory networks☆189Mar 9, 2024Updated 2 years ago
- ☆14Oct 24, 2025Updated 4 months ago
- R package for querying the DrugBank database in batch locally☆38Jul 30, 2021Updated 4 years ago
- trackc aims to produce beautiful genome tracks that are highly customizable☆16Jan 21, 2026Updated last month
- Using combined evidence from replicates to evaluate ChIP-seq peaks☆20Updated this week
- RNA-Seq normalization and quantification pipeline☆12Nov 25, 2024Updated last year
- Micro-C QC and data analysis☆16Aug 1, 2023Updated 2 years ago
- Single-Cell Spatial Explorer☆15Dec 14, 2023Updated 2 years ago
- ☆43Jan 26, 2026Updated last month
- scPred package for cell type prediction from scRNA-seq data☆99Jan 18, 2024Updated 2 years ago
- Gene Set + S2G strategy annotations analyzed for disease architecture☆59Nov 18, 2022Updated 3 years ago
- AD regulome analysis☆14Apr 4, 2023Updated 2 years ago
- QC report generator for Hi-C pairs file☆13Sep 14, 2020Updated 5 years ago