BART (Binding Analysis for Regulation of Transcription), a bioinformatics tool for inferring functional transcription factors (TFs) that bind at genomic cis-regulatory regions to regulate gene expression in the human or mouse genomes, given a query gene set or a ChIP-seq dataset as input. [Package] [Publication]
[BART web]

BART3D (BART for 3D genome data), a bioinformatics tool for inferring transcriptional regulators (TRs, including transcription factors and chromatin regulators) associated with differential chromatin interactions from Hi-C type 3D genome data for human or mouse. [Package] [Publication]

MARGE (Model-based Analysis of Regulation of Gene Expression), a comprehensive computational method for inference of cis-regulation of gene expression leveraging public H3K27ac genomic profiles in human or mouse. [Package] [Publication]

MANCIE (Matrix Analysis and Normalization by Concordant Information Enhancement), a computational method for high-dimensional genomic data integration. [Package] [Publication]

RECOGNICER (Recursive coarse-graining identification for ChIP-seq enriched regions), a ChIP-seq ultra-broad peak calling method. [Publication] [Source code] [Package built in SICER2]

SELMA (Simplex Encoded Linear Model for Accessible chromatin), a computational model for estimation and correction of intrinsic enzymatic cleavage biases in bulk and single-cell chromatin accessibility profiling (DNase-seq and ATAC-seq) data. [Package] [Publication]

SICER (Spatial-clustering Identification of ChIP-Enriched Regions), a ChIP-Seq data analysis method. [Package (v1.1)] [Publication]

SICER2 [Package (v2.0)]

BART Cancer, a database resource for computationally predicted transcriptional regulator activities in 15 human cancers from The Cancer Genome Atlas (TCGA). [Web resource] [Publication]