Application for making ENCODE Blacklists
☆334Apr 23, 2021Updated 4 years ago
Alternatives and similar repositories for Blacklist
Users that are interested in Blacklist are comparing it to the libraries listed below
Sorting:
- Detecting sites of genomic enrichment☆199May 8, 2023Updated 2 years ago
- ENCODE ATAC-seq pipeline☆446Jul 18, 2024Updated last year
- MACS -- Model-based Analysis of ChIP-Seq☆767Updated this week
- ChIP-seq analysis notes from Ming Tang☆842Aug 5, 2024Updated last year
- chromatin Variability Across Regions (of the genome!)☆185Jul 10, 2024Updated last year
- Tools to process and analyze deep sequencing data.☆751Jul 23, 2025Updated 7 months ago
- HMMRATAC peak caller for ATAC-seq data☆97Nov 12, 2024Updated last year
- Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal☆240Dec 2, 2025Updated 3 months ago
- Quick mining and visualization of NGS data by integrating genomic databases☆268May 5, 2023Updated 2 years ago
- ASCAT R package☆199Feb 12, 2026Updated 2 weeks ago
- A cool place to store your Hi-C☆231Feb 23, 2026Updated last week
- A collection of tools for Hi-C data analysis☆631Jan 31, 2026Updated last month
- Fast alignment and preprocessing of chromatin profiles☆213Jan 17, 2026Updated last month
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆826Feb 10, 2026Updated 2 weeks ago
- Genomic coordinates of problematic genomic regions as GRanges☆51Dec 10, 2025Updated 2 months ago
- IDR☆175Sep 18, 2018Updated 7 years ago
- ENCODE ChIP-seq pipeline☆277Feb 15, 2024Updated 2 years ago
- A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications☆41Feb 22, 2022Updated 4 years ago
- Analysis Pipeline for Single Cell ATAC-seq☆321Apr 27, 2023Updated 2 years ago
- BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy …☆73Dec 4, 2024Updated last year
- BigWig and BAM utilities☆103Mar 26, 2024Updated last year
- Chromatin State Maps in Mouse☆23May 16, 2018Updated 7 years ago
- FAN-C: Framework for the ANalysis of C-like data☆121Mar 13, 2024Updated last year
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆507Nov 6, 2025Updated 3 months ago
- Particle dynamics and simulated annealing for chromosome structure calculation☆28Mar 15, 2024Updated last year
- Intro to ChIPseq using HPC☆319Jan 30, 2023Updated 3 years ago
- python module to plot beautiful and highly customizable genome browser tracks☆864Jul 10, 2024Updated last year
- cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data☆144Apr 5, 2024Updated last year
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆447Feb 18, 2025Updated last year
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 6 months ago
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆52Apr 9, 2021Updated 4 years ago
- ChIP-seq peak-calling, QC and differential analysis pipeline.☆230Nov 21, 2025Updated 3 months ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated last year
- SEACR: Sparse Enrichment Analysis for CUT&RUN☆120Jan 15, 2023Updated 3 years ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆475Aug 31, 2025Updated 6 months ago
- A python extension for quick access to bigWig and bigBed files☆239Jan 14, 2026Updated last month
- Tools for handling Unique Molecular Identifiers in NGS data sets☆537Feb 2, 2026Updated last month
- make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.☆199Jan 30, 2026Updated last month
- Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.☆485Updated this week