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URL: https://code.google.com/p/ibm-cbc-genomic-tools/
Proper Citation: GenomicTools (RRID:SCR_001205)
Description: A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor.
Abbreviations: GenomicTools
Synonyms: GenomicTools: a computational platform for developing high-throughput analytics in genomics.
Resource Type: software resource
Defining Citation: PMID:22113082
Keywords: high-throughput sequencing, rna-seq, chip-seq, genomics, sequencing, hi-c, epigenetics, bio.tools
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