3 posts tagged with bioinformatics by grouse.
Displaying 1 through 3 of 3.

peaKO

We have created a new method to find transcription factor motifs in ChIP-seq data using knockout controls. Available on PyPI and GitHub.
posted by grouse on May 5, 2021 - 0 comments

Virtual ChIP-seq

Our new method predicts transcription factor and chromatin factor locations in a cell type using new kinds of data like chromatin factor binding in other cell types and learning the association of gene expression patterns with chromatin factor binding patterns. We've made free software available and a track hub that can load our predictions for 36 chromatin factors in 33 human tissue types into the UCSC Genome Browser.
posted by grouse on Feb 17, 2019 - 0 comments

Umap and Bismap: quantifying genome and methylome mappability

Many biological experiments use DNA sequencing as a readout. We can often map the sequenced DNA back to a specific region of the genome. Sometimes, however, we can't. Genomic data is less reliable in those regions. My lab has developed software that makes it easy to identify these regions. We also developed a new method that lets us find those regions in the context of bisulfite sequencing, a technique used to determine where DNA is chemically modified. [more inside]
posted by grouse on Dec 20, 2016 - 0 comments

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