GenomicTools
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Application data |
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| Created by | Aristotelis Tsirigos |
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| Biological application domain(s) | Genomics, ChIP-seq, RNA-Seq |
| Principal bioinformatics method(s) | Genome comparison, Peak calling, Heat map generation |
| Created at | IBM Research |
| Maintained? | Yes |
| Input format(s) | BED, SAM/BAM, GFF |
| Output format(s) | BED, SAM, GFF |
| Software features | create custom pipelines, feature overlaps, identify binding site peaks in ChIP-seq data, create read profiles, create read heatmaps |
| Programming language(s) | C, C++ |
| Licence | GPLv2 |
Summary: GenomicTools is a platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq.
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Description
GenomicTools is a flexible computational platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq. A variety of mathematical operations between sets of genomic regions is implemented thereby enabling the prototyping of computational pipelines that can address a wide spectrum of tasks from preprocessing and quality control to meta-analyses. More specifically, the user can easily 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.
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