Difference between revisions of "GenomicTools"
(Created page with "{{Bioinformatics application |sw summary=GenomicTools is a flexible computational platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq an...") |
|||
| Line 1: | Line 1: | ||
{{Bioinformatics application | {{Bioinformatics application | ||
| − | |sw summary=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. | + | |sw summary=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. |
| − | |bio domain=Genomics, ChIP-Seq, RNA-Seq, | + | |bio domain=Genomics, ChIP-Seq, RNA-Seq, |
| − | |bio method=genomic overlaps, | + | |bio method=genomic overlaps, peak detection, profiles, heatmaps |
|created by=Aristotelis Tsirigos | |created by=Aristotelis Tsirigos | ||
|created at=IBM Research | |created at=IBM Research | ||
|maintained=Yes | |maintained=Yes | ||
| − | |input format=BED, SAM/BAM, GFF, | + | |input format=BED, SAM/BAM, GFF, |
|output format=BED, SAM, GFF | |output format=BED, SAM, GFF | ||
| − | |sw feature= | + | |sw feature=create custom pipelines, feature overlaps, identify binding site peaks in ChIP-seq data, create read profiles, create read heatmaps |
|language=C/C++ | |language=C/C++ | ||
| − | |licence=GPL 2, | + | |licence=GPL 2, |
}} | }} | ||
== Description == | == Description == | ||
Revision as of 15:06, 13 April 2012
|
Application data |
|
| Created by | Aristotelis Tsirigos |
|---|---|
| Biological application domain(s) | Genomics, ChIP-Seq, RNA-Seq |
| Principal bioinformatics method(s) | genomic overlaps, peak detection, profiles, heatmaps |
| 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 | GPL 2 |
Summary: 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.
"Error: no local variable "counter" was set." is not a number.
Description
Links
References
To add a reference for GenomicTools, enter the PubMed ID in the field below and click 'Add'.
Search for "GenomicTools" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
