A modular, containerized pipeline for ATAC-seq data processing
☆60Feb 18, 2026Updated 2 weeks ago
Alternatives and similar repositories for pepatac
Users that are interested in pepatac are comparing it to the libraries listed below
Sorting:
- HMMRATAC peak caller for ATAC-seq data☆97Nov 12, 2024Updated last year
- A Feature Density Estimator for High-Throughput Sequence Tags☆22May 25, 2021Updated 4 years ago
- Project metadata manager for PEPs in Python☆40Jan 5, 2026Updated last month
- Predicting TF sequence-specificity similarity with weighted alignments☆13Oct 7, 2019Updated 6 years ago
- ENCODE ATAC-seq pipeline☆446Jul 18, 2024Updated last year
- R package to detect splicing QTLs (sQTLs)☆13Jul 3, 2023Updated 2 years ago
- Author academic documents in markdown☆12Oct 17, 2025Updated 4 months ago
- ☆27Oct 23, 2024Updated last year
- ☆13Updated this week
- ☆17Nov 9, 2020Updated 5 years ago
- Software to assemble contigs/scaffolds into chromosomes using Hi-C data☆28Sep 26, 2024Updated last year
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆12Oct 16, 2025Updated 4 months ago
- Application for making ENCODE Blacklists☆334Apr 23, 2021Updated 4 years ago
- TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.☆49Nov 16, 2022Updated 3 years ago
- code associated with crane-nature-2015, 10.1038/nature14450☆36Aug 28, 2015Updated 10 years ago
- qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Python☆21Sep 20, 2023Updated 2 years ago
- Code and figures accompanying the paper, "Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neu…☆20Jun 28, 2017Updated 8 years ago
- Modular job submitter for arbitrary pipelines or commands.☆24Updated this week
- a versatile and flexible pipeline for analysing different variants of ChIA-PET data☆36Nov 25, 2024Updated last year
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆72Apr 28, 2023Updated 2 years ago
- ChIP-seq and ATAC-seq analysis☆13Jun 17, 2024Updated last year
- Atac-seq QC matrix☆22Jun 4, 2024Updated last year
- Flexible and efficient tests for evidence of positive selection anywhere in the cancer genome.☆26Jul 30, 2022Updated 3 years ago
- SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data☆42Jul 6, 2023Updated 2 years ago
- A toolkit for working with ATAC-seq data.☆24Jan 22, 2026Updated last month
- The code for Daugherty, et al 2017 - Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans☆11Aug 24, 2017Updated 8 years ago
- abi2fastq is a small utility to convert Sanger sequencing reads in .abi (applied biosystems) format to FASTQ☆11Sep 19, 2017Updated 8 years ago
- ☆10Apr 30, 2019Updated 6 years ago
- ☆11Jul 31, 2019Updated 6 years ago
- A Nextflow DSL2 pipeline to perform ribo-seq data analysis and comprehensive quality control.☆19Dec 12, 2025Updated 2 months ago
- Code used for mouse single cell RNAseq testis atlas☆12Nov 28, 2020Updated 5 years ago
- A preprocessing and QC pipeline for HiChIP data☆40Jul 11, 2022Updated 3 years ago
- extract gene TSS/TES site form gencode/ensembl/gencode database GTF file and export bed format file.☆11Jan 24, 2022Updated 4 years ago
- SkewC a novel quality-assessment method to identify poor quality single-cells in scRNA-seq experiments. The method relies on the measure …☆10Aug 2, 2023Updated 2 years ago
- Paired Replicate Analysis of Allelic Differential Splicing Events☆12Feb 21, 2023Updated 3 years ago
- ATAC-seq and DNase-seq processing pipeline☆165Jun 21, 2022Updated 3 years ago
- Links to ATAC-seq analysis tools☆77Aug 24, 2021Updated 4 years ago
- STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data☆179Dec 18, 2021Updated 4 years ago
- Python toolkit for building restartable pipelines☆46Updated this week