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Popular tool citations

chevron_left Alternative splicing events identification Intron retention detection Exon skipping detection Alternative splicing visualization chevron_right
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SplicingViewer specifications

Information


Unique identifier OMICS_03519
Name SplicingViewer
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format (SAM, BAM) + (GFF, BED)
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.1.0
Stability Stable
Maintained No

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Publication for SplicingViewer

SplicingViewer in publications

 (4)
PMCID: 5294800
PMID: 28166730
DOI: 10.1186/s12864-017-3507-y

[…] of them under the developmental regulation., the transcriptome profile of v. dahliae in different growth conditions were investigated previously, and the alternative splicing was studied by using splicingviewer []. the study showed that over 95% of as events were intron retention, only ~1% of as events were exon skipping, a3ss or a5ss events in v. dahliae, respectively. though three ir events […]

PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] s1d in additional file ). sashimi, structure, and hive plots for splicing quantitative trait loci (sqtl) can be obtained using spliceplot []. splice graphs can be produced using spliceseq [], and splicingviewer [] plots splice junctions and alternative splicing events. trav [] is a visualization tool that integrates data analysis, but its analytical methods are not applicable to large […]

PMCID: 4549623
PMID: 26306464
DOI: 10.1038/srep13403

[…] china. tophat was used as an aligner to map the reads to the reference genome (n. crassa or74a (nc12)). cufflinks was used to reconstruct the transcripts and estimate the gene expression levels. the splicingviewer tool was used to annotate alternative splicing events. mixture of isoforms (miso) was used to estimate and compare the as event frequencies between samples. the bayes factors […]

PMCID: 4035056
PMID: 24884698
DOI: 10.1186/1471-2164-15-324

[…] the ms (figureĀ ).figure 8, alternative splicing (as) for the creation of new gene transcripts can increase regulatory complexity and control of developmental programs in higher organisms. a software splicingviewer [] was employed to identify putative as events in the six different developmental stages of v. dahliae that were examined in this study. this analysis tool enabled detection […]


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SplicingViewer institution(s)
Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, China; Beijing Institutes of Life Science, Chinese Academy of Science, Beijing, China
SplicingViewer funding source(s)
Supported by the National Natural Science Foundation of China (31171236/C060503) and the National Natural Science Foundation of China (31100917/C060503).

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