programmable-genomics/BATv1

As part of the ENCODE 4 Project, we trained BPNet models on 2,339 ENCODE transcription factor ChIP-seq experiments spanning 788 targets across 175 biosamples. Here, we provide all models for open-source use.

This is the first release of the Cherimoya Accessibility aTlas (CATv1): a collection of over 7,500 Cherimoya models trained on DNase-seq and ATAC-seq experiments from the ENCODE Project. Cherimoya models are state-of-the-art predictors of local chromatin accessibility, mapping a DNA sequence to a…

Resources on ChIP-seq data which include papers, methods, links to software, and analysis.

Predicts transcription factor binding sites in up to 316 vertebrate species by scoring JASPAR matrices against Ensembl promoter sequences and combining the match with seven contextual experimental datapoints, including evolutionary conservation, CAGE-defined transcription start sites, eQTLs, ChIP-seq peaks, ATAC-seq accessibility, DNase footprints and gene expression correlation, into a single score per site.

This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.

A diffusion language model for genome-scale perturbation prediction across diverse cellular contexts.