spliceR protocols

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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, plyr, RColorBrewer, IRanges, GenomicRanges, R(>=2.15.0), rtracklayer, BSgenome, BSgenome.Hsapiens.UCSC.hg19, VennDiagram, cummeRbund
Maintained Yes

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Publication for spliceR

spliceR in pipeline

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

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


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spliceR in publications

 (8)
PMCID: 5647428
PMID: 29044188
DOI: 10.1038/s41598-017-13887-y

[…] to gain detailed insight into gene specific splicing, we performed rna sequencing of three h3.3wt and three h3.3g34w primary gctb cell lines. using two different linux-based softwares, rmats and splicer, we found that exon skipping/inclusion were the most common aberration when comparing the two groups, additionally extending into the mutually exclusive exons-feature (fig. ). exon inclusion […]

PMCID: 5471846
PMID: 28615029
DOI: 10.1186/s13059-017-1243-x

[…] regression normalization approach []. fpkm was set at 1 as the threshold to minimize false positives in downstream analyses., the utr and alternative splicing analyses were performed using the splicer pipeline [, ]. in brief, potential coding dna sequences (cds) were first determined by splicer, and both 5′ and 3′ utr sequences were then extracted for utr length analyses. to validate […]

PMCID: 5457400
PMID: 28578384
DOI: 10.1038/s41598-017-02970-z

[…] high differential expression. to define the functions of the identified genes, we used moss genome annotation 1.6 (http://www.cosmoss.org) and blast search against annotated a. thaliana sequences., splicer was used with default settings to annotate transcripts with classes of as event. briefly, based on the information from all transcripts originating from a single gene, splicer constructs […]

PMCID: 5347137
PMID: 28276441
DOI: 10.1038/ncomms14749

[…] with the same method that was used for analysing our sequencing data. for neuronal iis transcriptome data analysis, we removed low-quality samples., ptcs were defined using the bioconductor package splicer 1.14.0 with default parameters. briefly, ptcs were annotated when stop codons were located more than 50 nt upstream of the final exon–exon junctions., potential orfs were estimated […]

PMCID: 5331056
PMID: 28298916
DOI: 10.3389/fpls.2017.00267

[…] method. bonferrony correction was employed for p-value correction with a cut-off of 0.05. to identify alternative splicing events associated with drought stress, cuffdiff data was analyzed using the splicer module in r (vitting-seerup et al., )., rna isolated from the ww and ds groups was used to construct a cdna library. first-strand synthesis was performed using the primescript first strand […]


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

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