pinellolab/haystack_bio repository overview

Haystack is a suite of computational tools implemented in a Python 2.7 package called haystack_bio to study epigenetic variability, cross-cell-type plasticity of chromatin states and transcription factors (TFs) motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation.

Through the integration of epigenomic, DNA sequence, and gene expression data, haystack_bio identifies highly variable regions across different cell types (called hotspots) and the potential regulators that mediate the cell-type specific variation.

haystack_bio can be used with histone modifications and chromatin accessibility data generated by ChIP-seq, DNase-Seq, and ATAC-seq assays across multiple cell-types. In addition, it is also possible to integrate gene expression data generated by RNA-seq for example. In particular, haystack_bio highlights enriched TF motifs in variable and cell-type specific regions and quantifies their activity and specificity on nearby genes if gene expression data are available.

The full documentation is hosted here: https://github.com/pinellolab/haystack_bio⁠