More software can be found in our GitHub Repository.
EC2-launcher - A tool that lauches docker jobs on Amazon EC2.
GERV - A statistical method for predicting non-coding variants’ effect on transcription factor binding.
PIQ - A computational method that identifies the genomic binding sites of hundreds of transcription factors (TFs) at corresponding motifs from DNase-Seq experiments with accuracy comparable to ChIP-Seq.
GERM - An approach to identifying conditional occupancy events for a protein from ChIA-PET data.
SRPOUT - High Resolution Modeling of Chromatin Interactions.
Fixseq - A over-dispersion correction technique that serves as a smarter way to de-duplicate counts.
Multipool - High-resolution genetic mapping for pooled sequencing
GEM - Integrative Genome wide Event finding and Motif discovery for ChIP-seq and ChIP-exo data.
GPS - The Genome Positioning System for discovering binding events in ChIP-seq data.
GSE - Genomic Spatial Events system, a database for storing, visualizing, and analyzing ChIP-base transcription factor binding data and gene expression data.
GRAM - The GRAM (Genetic RegulAtory Modules) algorithm identifies modules, collections of genes that share common regulators, as well as expression profiles.
JBD - The JBD (Joint Binding Deconvolution) algorithm detects binding sites based on ChIP-chip data and guides.
GeneProgram - Automated discovery of functional generality of gene expression programs (sets co-expressed genes)