Predicts transcription factors binding sites and epigenetic data by combining sets of open-chromatin regions with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. It computes transcription factors affinities and uses open-chromatin / Histone-Mark signal intensity as quantitative measures of transcription factor (TF) binding strength. The tool outperforms several competitive approaches.
Automates the processing and analysis of several commonly used Next Generation Sequencing (NGS) datasets including: ChIP-seq, RNA-seq, Global Run On sequencing (GRO-seq), micrococcal nuclease footprint sequencing (MNase-seq), DNase hypersensitivity sequencing (DNase-seq), and transposase-accessible chromatin using sequencing ATAC-seq datasets. CIPHER provides an analysis mode that accomplishes complex bioinformatics tasks such as enhancer prediction. It supplies functions to integrate various NGS datasets together.
Provides a pipeline for executing chromatin profiling assays. ATAC2GRN gathers optimized ATAC-seq and DNase1-seq pipelines to assess accurate genome regulatory network (GRN) inference. This software assists for maximizing ChIP recovery for transcription factor occupancy assessment. The project is composed of three main parts: one to generate figures, one part in both bash and Snakemake for the pipelines and the last one to estimate pipeline recapitulation of ChIP-seq.
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