Difference between revisions of "FindPeaks 4.0 (Vancouver Short Read Package)"
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|sw summary=The Vancouver Short Read Analysis Package (VSRAP) contains the FindPeaks application for Chip-Seq and RNA-Seq analysis, as well as utilities for SNP finding, working with aligned sequence files and a nascent database for storing SNPs across multiple libraries. | |sw summary=The Vancouver Short Read Analysis Package (VSRAP) contains the FindPeaks application for Chip-Seq and RNA-Seq analysis, as well as utilities for SNP finding, working with aligned sequence files and a nascent database for storing SNPs across multiple libraries. | ||
|bio domain=Genomics,SNP discovery, | |bio domain=Genomics,SNP discovery, | ||
| − | |bio method=Peak calling, Database, Format conversion, | + | |bio method=Peak calling, Database, Format conversion, Sequence alignment analysis |
|created by=Anthony Fejes | |created by=Anthony Fejes | ||
|created at=BC Genome Sciences Centre, Sourceforge, | |created at=BC Genome Sciences Centre, Sourceforge, | ||
Revision as of 12:44, 3 November 2015
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Application data |
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| Created by | Anthony Fejes |
|---|---|
| Biological application domain(s) | Genomics, SNP discovery |
| Principal bioinformatics method(s) | Peak calling, Database, Format conversion, Sequence alignment analysis |
| Created at | BC Genome Sciences Centre, Sourceforge |
| Maintained? | Yes |
| Input format(s) | BED, Maq, SAM, Bowtie, Eland, FASTA, Mapview |
| Output format(s) | ACE, BED, GFF, WIG, Peaks, Regions, PNG |
| Software features | command line |
| Programming language(s) | Java |
| Licence | GPL |
| Operating system(s) | Linux, Windows, Mac OS X |
Summary: The Vancouver Short Read Analysis Package (VSRAP) contains the FindPeaks application for Chip-Seq and RNA-Seq analysis, as well as utilities for SNP finding, working with aligned sequence files and a nascent database for storing SNPs across multiple libraries.
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This package includes a growing suite of open source tools for working with Aligned reads of a wide variety of formats. The original version began with the FindPeaks ChIP-Seq tool, but has since grown into a wide variety of tools covering features from ChIP-Seq to RNA-Seq analysis and SNP discovery.
Contributions are welcome and encouraged, and new developers are welcome to join the project.
Links
References
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