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Protocols

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

 (7)
library_books

Advanced Applications of RNA Sequencing and Challenges

2015
Bioinform Biol Insights
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 and model […]

library_books

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

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

[…] current 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., Cuffdiff2 […]

library_books

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

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

[…] ed 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 speci […]

library_books

RAX2: a genome wide detection method of condition associated transcription variation

2015
Nucleic Acids Res
PMCID: 4551904
PMID: 25953852
DOI: 10.1093/nar/gkv411

[…] f these isoforms from the transcription unit as a single entity and applying statistical approaches DESeq (), baySeq (), edgeR exact test (,), edgeR GLM (), DEXSeq (), Cuffdiff (,), DiffSplice () and SplicingCompass () to determine whether a given isoform is differentially expressed between two different cell states. However, these approaches do not directly assess whether isoforms within genes ar […]

call_split

Algorithms for differential splicing detection using exon arrays: a comparative assessment

2015
BMC Genomics
PMCID: 4391533
PMID: 27391904
DOI: 10.1186/s12864-015-1322-x
call_split See protocol

[…] ion. Deviation from exon to gene expression results in low correlation and therefore indicates DS. ANOSVA detects DS by applying statistical tests to the parameters of a fitted exon expression model. SplicingCompass, originally developed for NGS data, can easily be adapted to exon array data. The idea is to access the significance of difference between angles spanned by exon tuples in one conditio […]

library_books

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

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

[…] he AUC statistics and the methods’ rankings based on the AUC (Table ). Even for the recall and precision statistics (Table ), the increase in sample size had a small impact for all methods except for SplicingCompass and SeqGSEA. Recall for SplicingCompass increased from 14% to 50% when the sample size increased from 3 to 8. SeqGSEA was not statistically significant at FDR=0.05 for a sample size of […]

Citations

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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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