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Motif elucidation in ChIP-seq datasets with a knockout control | PeaKO discovers motifs in ChIP-seq datasets with knockout controls. PeaKO takes in paired wild-type/knockout BAM files in addition to several reference files, as input. It returns a file of ranked motifs (see our paper for more details) | PeaKO finding transcription factor binding motifs using knockout controls | Denisko D, Viner C, Hoffman MM. Motif elucidation in ChIP-seq datasets with a knockout control. BioRxiv 10.1101/721720 [Preprint]. 2019. Available from: https://doi.org/10.1101/721720 | PeaKO identifies motifs relevant to ChIP-seq experiments by combining two differential analysis approaches. It often improves elucidation of the target motif over other methods and highlights the benefits of knockout controls

Bedshift is a tool for randomly perturbing BED file regions. The perturbations supported on regions are shift, drop, add, cut, and merge. This tool is particularly useful for creating test datasets for various tasks, since there often is no ground truth dataset to compare to. By perturbing a file, a pipeline or analysis can be run on both the perturbed file and the original file, then be compared.

BART3D is a computational method for inferring transcriptional regulators (TRs) associated with genome-wide differential chromatin interactions (DCIs) detected by comparing two Hi-C maps. And Inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data.

MAnorm2 for quantitatively comparing groups of ChIP-seq samples. To pre-process a set of ChIP-seq samples. MAnorm2_utils is designed to coordinate with MAnorm2, an R package for differential analysis with ChIP-seq signals between two or more groups of replicate samples. MAnorm2_utils is primarily used for processing a set of ChIP-seq samples into a regular table recording the read abundances and enrichment states of a list of genomic bins in each of these samples.