Software

More software can be found in our GitHub Repository.

• EC2-launcher - A tool that lauches docker jobs on Amazon EC2.

• Caffe-cnn - A Caffe-based deep learning platform with automatic hyper-parameter searching.

• 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 (download page)

• GEM / KSM and KMAC - A novel motif representation for transcription factor binding, K-mer Set Memory

• GEM / CID - Chromatin Interaction Discovery for ChIA-PET and HiChIP data

• GEM / RMD - Regulatory Module Discovery - Discovery of transcription factor co-binding patterns

• 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)