SpliceSeq statistics

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Citations per year

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Popular tool citations

chevron_left Differential expression Normalization Alternative splicing events identification Known transcript quantification Spliced read alignment Alternative splicing visualization chevron_right
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Associated diseases

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SpliceSeq specifications

Information


Unique identifier OMICS_01267
Name SpliceSeq
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input format FASTA, FASTQ
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Michael C. Ryan <>

Publication for SpliceSeq

SpliceSeq in publications

 (10)
PMCID: 5899436
PMID: 29581274
DOI: 10.1073/pnas.1714573115

[…] and drug design., to investigate as patterns among various breast cancer subtypes, we downloaded percent spliced in (psi) values for breast cancer splice events from the cancer genome atlas (tcga) spliceseq, a web-based resource (). a total of 45,421 splice events from 10,480 expressed genes were acquired from 1,094 available samples representing four breast cancer subtypes (luminal a, luminal […]

PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] in 85 genes overlapped with events reported for acute myeloid leukemia (aml) and 105 exons in 67 genes overlapped with events reported for diffuse large b-cell lymphoma (dlbcl) according to the tcga spliceseq data base. alternative splicing events in 56 genes are overlapping between all 3 hematologic malignancies (t-pll, aml, and dlbcl)., t-pll tumor singles of 18 cases were analyzed […]

PMCID: 5931977
PMID: 29429992
DOI: 10.1038/s41388-017-0119-6

[…] asked whether srsf10 executed its oncogenetic effects by regulating as in cc. to test this hypothesis, we first analyzed srsf10-related as events in cc by utilizing the cancer genome atlas (tcga) spliceseq data set (http://bioinformatics.mdanderson.org/tcgaspliceseq/) (supplementary fig. ) []. in cc, 3137 as events were related to srsf10 expression, which were essentially the inclusion […]

PMCID: 5787501
PMID: 29416646
DOI: 10.18632/oncotarget.21672

[…] and polysome-bound mrna (the translatome) of the human glioblastoma stem-like cell line nsc11. for these studies, rna-seq profiles from control and irradiated cells were compared using the program spliceseq to identify transcripts and splice variations induced by radiation. as compared to the transcriptome (total rna) of untreated cells, the radiation-induced transcriptome contained 92 splice […]

PMCID: 5129602
PMID: 27899088
DOI: 10.1186/s12885-016-2928-3

[…] if the score was above the median value of all samples and negative otherwise., the alternative splicing of era was generated from rna-seq data which were acquired from tcga data portal by tcga spliceseq database []. based on the coverage of different splicing isoforms, each alternative splicing event was assigned with a psi (percent spliced in) value ranging from 0 to 1. to increase […]


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SpliceSeq institution(s)
In Silico Solutions, Fairfax, VA; Department of Bioinformatics and Computational Biology and Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

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