From 9eab87a2f02d0e611b7122b9d2c872b9d1d8f0f8 Mon Sep 17 00:00:00 2001 From: Ming Tang Date: Thu, 10 May 2018 10:33:56 -0500 Subject: [PATCH] add diff ATACseq --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 007fe98..3dcc046 100644 --- a/README.md +++ b/README.md @@ -400,6 +400,7 @@ A paper from Genome Research [Ubiquitous heterogeneity and asymmetry of the chro * [Brockman](https://carldeboer.github.io/brockman.html) is a suite of command line tools and R functions to convert genomics data into DNA k-mer words representing the regions associated with a chromatin mark, and then analyzing these k-mer sets to see how samples differ from each other. This approach is primarily intended for single cell genomics data, and was tested most extensively on single cell ATAC-seq data * [Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling](https://www.biorxiv.org/content/early/2018/03/19/284364) * [msCentipede](http://rajanil.github.io/msCentipede/) is an algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data (Dnase-seq, ATAC-seq) and is written in Python2.x and Cython. +* The Differential ATAC-seq Toolkit [(DAStk)](https://biof-git.colorado.edu/dowelllab/DAStk) is a set of scripts to aid analyzing differential ATAC-Seq data. ### DNase-seq * [pyDNase](/~https://github.com/jpiper/pyDNase) - a library for analyzing DNase-seq data. [paper: Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors](http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2081-4)