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SplicingCompass specifications

Information


Unique identifier OMICS_01340
Name SplicingCompass
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Read count and junctions
Input format GFF + BED
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained No

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Publication for SplicingCompass

SplicingCompass citations

 (5)
library_books

Advanced Applications of RNA Sequencing and Challenges

2015
PMCID: 4648566
PMID: 26609224
DOI: 10.4137/BBI.S28991

[…] de novo assembly and characterization of transcript models. examples of these methods are miso for identification and regulation of isoforms from clip-seq data and splicemap, splitseek, splicer, and splicingcompass for detection of splice junctions and exon usage from pair-end rna-seq. glimmps provides a useful tool for elucidating the genetic variation of alternative splicing in humans […]

library_books

Evaluation of methods for differential expression analysis on multi group RNA seq count data

2015
PMCID: 4634584
PMID: 26538400
DOI: 10.1186/s12859-015-0794-7

[…] de analysis: gene-, transcript-, exon-, and base-level. examples of the de methods for individual levels are (i) edger [], deseq [], and tcc [] for gene-level; (ii) cuffdiff2 [], iuta [], and splicingcompass [] for transcript-level; (iii) dexseq [] and npebseq [] for exon-level; and (iv) der finder [] for base-level. many methods can perform de analysis for multiple levels (e.g., […]

library_books

RNA Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq

2015
PMCID: 4556662
PMID: 26327458
DOI: 10.1371/journal.pone.0136653

[…] for alternative expression analysis of genetic features including exon regions, exon junctions, and intron regions []. other software tools designed for alternative splicing analysis include mats, splicingcompass, and juncbase [–]., dexseq is an r bioconductor package that is widely used in differential expression analysis of exons []. dexseq applies generalized linear models and identifies […]

library_books

Defining the transcriptomic landscape of Candida glabrata by RNA Seq

2015
PMCID: 4330350
PMID: 25586221
DOI: 10.1093/nar/gku1357

[…] were calculated and then used to apply a 2-fold-change filter., for the detection of significantly differentially expressed isoforms (deis), the mapped reads were utilized with the tools mats (), splicingcompass () and diffsplice (). results with a false discovery rate value < 0.05 were considered significant. all splicing events were manually checked using integrative genomics viewer ()., […]

library_books

Comparisons of computational methods for differential alternative splicing detection using RNA seq in plant systems

2014
PMCID: 4271460
PMID: 25511303
DOI: 10.1186/s12859-014-0364-4

[…] classification nomenclature defined by pachter in []. we selected eight methods and evaluated them based on simulated and real data. six of them are from count-based models: dexseq [], dsgseq [], splicingcompass [], mats [], rdiff-parametric [] and seqgsea []. the remaining two, cufflinks [] and diffsplice [], use isoform resolution models. a brief overview of the eight methods follows.figure […]


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SplicingCompass institution(s)
Bioinformatics HUSAR, Genomics Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Theoretical Bioinformatics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology and Hematology and Center for Molecular Medicine Cologne (CMMC), University Children’s Hospital, Cologne, Germany; Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany; Center for Sepsis Control and Care, University Hospital Jena, Jena, Germany; Leibniz Institute for Natural Products Research and Infection Biology, Hans-Knoll-Institute, Jena, Germany
SplicingCompass funding source(s)
This project was supported by the Joint Germany-Israeli Research Program (ca-139) (DKFZ/MOST), the Nationales Genom-Forschungs-Netz (NGFN+), ENGINE (#01GS0898).

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