a peak-calling and differential analysis tool for replicated ChIP-Seq data
☆37May 18, 2022Updated 4 years ago
Alternatives and similar repositories for PePr
Users that are interested in PePr are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Wrappers around NGS peak callers to both call peaks and run IDR☆11Aug 2, 2013Updated 13 years ago
- ☆11Dec 3, 2013Updated 12 years ago
- Enriched Domain Detector for ChIP-seq data☆16Aug 17, 2022Updated 4 years ago
- MUltiScale enrIchment Calling for ChIP-Seq Datasets☆23Mar 14, 2019Updated 7 years ago
- SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis☆25Apr 7, 2015Updated 11 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- SPP - R package for analysis of ChIP-seq and other functional sequencing data☆43Jul 6, 2021Updated 5 years ago
- Chromatin segmentation in R☆19Feb 4, 2018Updated 8 years ago
- A versatile and efficient RNA-Seq read counting tool☆16Mar 30, 2016Updated 10 years ago
- Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data☆85Aug 25, 2020Updated 6 years ago
- PARE: a computational method to Predict Active Regulatory Elements☆11Aug 8, 2025Updated last year
- Hotspot is a program for identifying genomic regions of local enrichment of short-read sequence tags.☆16Apr 12, 2014Updated 12 years ago
- Romulus: Robust multi-state identification of transcription factor binding sites from DNase-seq data☆10Mar 6, 2019Updated 7 years ago
- Python wrapper around the popular ChIP-Seq peak caller SICER☆15Dec 7, 2017Updated 8 years ago
- Differential analysis for ChIP-seq with biological replicates☆35Jan 5, 2022Updated 4 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Peakzilla is a self-learning algorithm to identify transcription factor binding sites from ChIP-seq data. I would be very happy if you tr…☆21Aug 18, 2025Updated last year
- Normalization and difference calling for Next Generation Sequencing (NGS) data via joint multinomial modeling.☆11May 21, 2026Updated 5 months ago
- Ritornello is a high fidelity control free ChIP-seq peak calling algorithm☆13Aug 23, 2018Updated 8 years ago
- Q ChIP-seq peak caller☆18Jul 17, 2024Updated 2 years ago
- 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
- A tool to identify, annotate and visualise splicing switch events from RNA-seq data☆14Aug 26, 2015Updated 11 years ago
- ☆10Jan 8, 2018Updated 8 years ago
- Blacktie: a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline☆26Oct 5, 2015Updated 11 years ago
- ChromDiff program as described in Yen and Kellis, Nature Communications 2015.☆14May 12, 2016Updated 10 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.
- (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER☆31Nov 21, 2018Updated 7 years ago
- Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway …☆26Dec 11, 2017Updated 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
- COMETgazer mehylation analysis software suite☆10Jul 21, 2019Updated 7 years ago
- Applying IDR analysis to Homer peaks.☆20May 8, 2020Updated 6 years ago
- This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…☆62Jul 20, 2020Updated 6 years ago
- Rcount: simple and flexible RNA-Seq read counting☆12May 19, 2022Updated 4 years ago
- Code for finding putative enhancers using Hi-C data☆28Feb 27, 2018Updated 8 years ago
- DEPRECATED Lightweight bioinformatics pipeline tools using iPython☆14Dec 11, 2015Updated 10 years ago
- AI Agents on 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.
- A python script used to annotate genomic intervals.☆18May 29, 2020Updated 6 years ago
- ☆12Sep 10, 2026Updated last month
- Download binary executables and sample data here:☆18Oct 28, 2016Updated 10 years ago
- ☆13Apr 14, 2026Updated 6 months ago
- R package to quickly obtain count vectors from indexed bam files☆15May 21, 2026Updated 5 months ago
- CONICS: COpy-Number analysis In single-Cell RNA-Sequencing☆78Feb 27, 2023Updated 3 years ago
- significance testing over interval overlaps☆30Jul 11, 2020Updated 6 years ago