This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
☆62Jul 20, 2020Updated 5 years ago
Alternatives and similar repositories for phantompeakqualtools
Users that are interested in phantompeakqualtools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- IDR☆175Sep 18, 2018Updated 7 years ago
- Python wrapper around the popular ChIP-Seq peak caller SICER☆15Dec 7, 2017Updated 8 years ago
- MUltiScale enrIchment Calling for ChIP-Seq Datasets☆23Mar 14, 2019Updated 7 years ago
- software for analysis of chromatin feature occupancy profiles from high-throughput sequencing data☆18Nov 26, 2019Updated 6 years ago
- SPP - R package for analysis of ChIP-seq and other functional sequencing data☆44Jul 6, 2021Updated 4 years ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Ritornello is a high fidelity control free ChIP-seq peak calling algorithm☆13Aug 23, 2018Updated 7 years ago
- ☆24Feb 24, 2025Updated last year
- Published methods☆15Oct 19, 2016Updated 9 years ago
- AQUAS TF and histone ChIP-seq pipeline☆112Jun 21, 2022Updated 3 years ago
- Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post…☆27Oct 14, 2025Updated 5 months ago
- Bedfile perturbation tool☆17Mar 6, 2026Updated 3 weeks ago
- ENCODE ChIP-seq pipeline☆277Feb 15, 2024Updated 2 years ago
- MACS -- Model-based Analysis of ChIP-Seq☆770Mar 19, 2026Updated last week
- Analysis and Visualization of Ribosome Profiling Data☆12Dec 14, 2019Updated 6 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Applying IDR analysis to Homer peaks.☆15May 8, 2020Updated 5 years ago
- ChIP-seq analysis notes from Ming Tang☆846Aug 5, 2024Updated last year
- make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.☆200Jan 30, 2026Updated last month
- Ultraperformant reimplementation of SICER☆59Dec 1, 2025Updated 3 months ago
- JAMM Peak Finder for Sequencing Datasets☆30Mar 12, 2020Updated 6 years ago
- A collection of perl scripts for NGS analysis☆17Oct 2, 2024Updated last year
- a peak-calling and differential analysis tool for replicated ChIP-Seq data☆37May 18, 2022Updated 3 years ago
- python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.☆15Feb 13, 2018Updated 8 years ago
- yaha: a flexible, sensitive and accurate DNA alignment tool designed to find optimal split-read mappings on single-end queries from 100bp…☆20Dec 6, 2017Updated 8 years ago
- NordVPN Special Discount Offer • AdSave on top-rated NordVPN 1 or 2-year plans with secure browsing, privacy protection, and support for for all major platforms.
- AlignerBoost is a generalized software toolkit for boosting Next-Gen sequencing mapping precision using a Bayesian based mapping quality …☆11Mar 1, 2022Updated 4 years ago
- Tools for querying and analysis of genomic data☆27Oct 26, 2025Updated 5 months ago
- ☆17Jan 3, 2019Updated 7 years ago
- Detecting Regulatory Elements using GRO-seq and PRO-seq☆40Apr 30, 2025Updated 10 months ago
- Genomic plot in trellis layout☆43Jan 30, 2026Updated last month
- Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.☆112Nov 3, 2025Updated 4 months ago
- ☆95Jul 6, 2025Updated 8 months ago
- SeqPlots - An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and he…☆87May 11, 2022Updated 3 years ago
- fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome☆158Aug 8, 2025Updated 7 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Download binary executables and sample data here:☆18Oct 28, 2016Updated 9 years ago
- Basic workflow for ATAC-seq analysis☆95Feb 23, 2024Updated 2 years ago
- Differential analysis for ChIP-seq with biological replicates☆35Jan 5, 2022Updated 4 years ago
- (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER☆31Nov 21, 2018Updated 7 years ago
- ENCODE Uniform processing pipeline for ChIP-seq☆124Mar 23, 2020Updated 6 years ago
- COMETgazer mehylation analysis software suite☆10Jul 21, 2019Updated 6 years ago
- Software for predicting library complexity and genome coverage in high-throughput sequencing.☆94Dec 24, 2025Updated 3 months ago