Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
☆112May 14, 2026Updated 2 months ago
Alternatives and similar repositories for cutandrun
Users that are interested in cutandrun are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ATAC-seq peak-calling and QC analysis pipeline☆226Jul 6, 2026Updated 2 weeks ago
- Analytical pipeline developed to anlayze Cut and Run data. Inspired by both Henikoff (SEACR) and Orkin (Cut&RunTools) lab pipelines.☆20May 26, 2025Updated last year
- SEACR: Sparse Enrichment Analysis for CUT&RUN☆122Jan 15, 2023Updated 3 years ago
- CUT&RUN and CUT&Tag data processing and analysis☆114Mar 4, 2025Updated last year
- ☆14Mar 28, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ChIP-seq peak-calling, QC and differential analysis pipeline.☆242Updated this week
- A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted nex…☆61Jun 22, 2026Updated last month
- ATAC-seq lab for BIOINF525☆10Mar 31, 2016Updated 10 years ago
- Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague☆14Aug 19, 2020Updated 5 years ago
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆343Jul 13, 2026Updated last week
- R package for nucleotide conversion sequencing data analysis☆17Jan 13, 2026Updated 6 months ago
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆1,342Jul 16, 2026Updated last week
- Analysis of Chromosome Conformation Capture data (Hi-C)☆110May 6, 2026Updated 2 months ago
- Nascent Transcription Processing Pipeline☆23Updated this week
- 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.
- ☆33Jul 20, 2018Updated 8 years ago
- Tutorial Website☆67Feb 1, 2021Updated 5 years ago
- Pipeline to fetch metadata and raw FastQ files from public databases☆196May 29, 2026Updated last month
- ATAC-seq Quality Control☆27Jul 13, 2026Updated last week
- Example scripts for analyzing CUT&RUN datasets☆13Oct 3, 2018Updated 7 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Jun 7, 2019Updated 7 years ago
- ENCODE ChIP-seq pipeline☆283Feb 15, 2024Updated 2 years ago
- Pipeline for Cut&Tag analysis☆25Apr 15, 2025Updated last year
- Intro to ChIPseq using HPC☆324Jan 30, 2023Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ☆18May 12, 2023Updated 3 years ago
- gatk4 RNA variant calling pipeline☆61Jul 8, 2026Updated 2 weeks ago
- Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing☆30Dec 13, 2024Updated last year
- Luslab nextflow modules☆14Apr 30, 2021Updated 5 years ago
- ☆10Mar 11, 2025Updated last year
- ☆13Jul 26, 2022Updated 3 years ago
- JEME method for predicting enhancer targets☆11Jul 15, 2017Updated 9 years ago
- MACS -- Model-based Analysis of ChIP-Seq☆781Jul 7, 2026Updated 2 weeks ago
- Improved Ribo-seq enables identification of cryptic translation events☆17Feb 13, 2018Updated 8 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A modular Hi-C mapping pipeline☆105Dec 5, 2024Updated last year
- A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications☆42Jun 30, 2026Updated 3 weeks ago
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆583Updated this week
- Pipeline for the identification of (coding) gene structures in draft genomes.☆38May 9, 2024Updated 2 years ago
- Materials presented at the BiocNYC meet-up☆12Nov 29, 2018Updated 7 years ago
- your friendly pangenome graph genotyper☆10Feb 6, 2023Updated 3 years ago
- Detection of m6A from direct RNA-Seq data☆133May 19, 2025Updated last year