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Repository seacr
Name: seacr
Owner: iuc
Synopsis: SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.
CUT&RUN is an efficient epigenome profiling method that identifies sites of DNA binding protein enrichment genome-wide with high signal to noise and low sequencing requirements. Currently, the analysis of CUT&RUN data is complicated by its exceptionally low background, which renders programs designed for analysis of ChIP-seq data vulnerable to oversensitivity in identifying sites of protein binding.

Here we introduce Sparse Enrichment Analysis for CUT&RUN (SEACR), an analysis strategy that uses the global distribution of background signal to calibrate a simple threshold for peak calling. SEACR discriminates between true and false-positive peaks with near-perfect specificity from gold standard CUT&RUN datasets and efficiently identifies enriched regions for several different protein targets.

SEACR is a highly selective peak caller that definitively validates the accuracy of CUT&RUN for datasets with known true negatives. Its ease of use and performance in comparison with existing peak calling strategies make it an ideal choice for analyzing CUT&RUN data.
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Contents of this repository

Name Description Version Minimum Galaxy Version
for sparse enrichment analysis 1.3+galaxy0 16.01

Epigenetics - Tools for analyzing Epigenetic/Epigenomic datasets
ChIP-seq - Tools for analyzing and manipulating ChIP-seq data.