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add diff ATACseq
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crazyhottommy authored May 10, 2018
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Expand Up @@ -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)
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