spliceR protocols

spliceR specifications

Information


Unique identifier OMICS_03514
Name spliceR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.3.1
Stability Stable
Requirements methods, cummeRbund, rtracklayer, VennDiagram, RColorBrewer, plyr
Maintained Yes

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Publication for spliceR

spliceR IN pipelines

 (2)
2018
PMCID: 5810112
PMID: 29433555
DOI: 10.1186/s13045-018-0558-8

[…] the curated gene sets of canonical pathways [33, 34]. differentially expressed genes were extracted using the cummerbund r package. differentially spliced genes where annotated and extracted using splicer [35]., to explore the role of sf3b1 in human erythropoiesis, we first examined the expression of sf3b1 in highly purified erythroid cells at each distinct developmental stage derived […]

2017
PMCID: 5319189
PMID: 28219335
DOI: 10.1186/s12870-017-0996-4

[…] an important form of regulation in plant development and environmental responses [25, 26]. from our transcriptome data, a gene was considered alternatively spliced if it was identified by cuffdiff2/splicer [27, 28] as having differential isoform expression and by junctionseq [29] as having differential exon or splice junction usage. using this methodology, there were 30, 139, and 470 genes […]

spliceR institution(s)
Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, DK, Denmark

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