Difference between revisions of "FeatureCounts"
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|sw summary=featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. | |sw summary=featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. | ||
|bio domain=Next Generation Sequencing | |bio domain=Next Generation Sequencing | ||
| − | |bio method=Read | + | |bio method=Read summarisation, |
|bio tech=Illumina, 454, ABI SOLiD, Ion Torrent, | |bio tech=Illumina, 454, ABI SOLiD, Ion Torrent, | ||
|created by=Wei Shi and Yang Liao | |created by=Wei Shi and Yang Liao | ||
| Line 10: | Line 10: | ||
|input format=SAM/BAM, | |input format=SAM/BAM, | ||
|output format=an R List object (in R) or a text file including read counts (in command line) | |output format=an R List object (in R) or a text file including read counts (in command line) | ||
| − | |sw feature=read | + | |sw feature=read summarisation |
|language=R, C | |language=R, C | ||
|licence=GPLv3 | |licence=GPLv3 | ||
Latest revision as of 18:44, 2 December 2015
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Application data |
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| Created by | Wei Shi and Yang Liao |
|---|---|
| Biological application domain(s) | Next Generation Sequencing |
| Principal bioinformatics method(s) | Read summarisation |
| Technology | Illumina, 454, ABI SOLiD, Ion Torrent |
| Created at | Australia
The Walter and Eliza Hall Institute |
| Maintained? | Yes |
| Input format(s) | SAM/BAM |
| Output format(s) | an R List object (in R) or a text file including read counts (in command line) |
| Software features | read summarisation |
| Programming language(s) | R, C |
| Licence | GPLv3 |
| Operating system(s) | Linux 64, Mac OS X, Mac OS X; x86 64 |
Summary: featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.
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