UCSC Xena protocols

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description
UCSC Xena computational protocol

UCSC Xena specifications

Information


Unique identifier OMICS_17671
Name UCSC Xena
Interface Web user interface
Restrictions to use None
Programming languages Javascript, Shell (Bash), Other
License Apache License version 2.0
Computer skills Basic
Version 0.21.0
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline UCSC Xena Team <>

Information


Unique identifier OMICS_17671
Name UCSC Xena
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline UCSC Xena Team <>

Publication for UCSC Xena

UCSC Xena IN pipelines

 (2)
2018
PMCID: 5820260
PMID: 29463849
DOI: 10.1038/s41598-018-20321-4

[…] without restrictions on their use in publications or presentations. single nucleotide variants (snv) for these kirc samples were subsequently annotated by oncotator36 in ucsc cancer browser (ucsc xena now). after removing hyper mutated samples, we transformed them to a 0/1 matrix (patient x mutation gene) and filtered low mutation frequency (<3) genes in order to lessen bias. […]

2018
PMCID: 5930504
PMID: 29744254
DOI: 10.1186/s40164-018-0102-0

[…] expression, mirna expression as well as clinical information (when available) from prca and matched normal patient samples generated by the cancer genome atlas (tcga) consortium were retrieved from ucsc xena browser [24]. it comprises mrnaseq level_3 data (file names: *.rsem.genes.normalized_results) of 550 samples, mirnaseq data level_3 data (file names: *.isoform.quantification.txt) of 544 […]

UCSC Xena institution(s)
UCSC Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA; BITS Pilani KK Birla Goa Campus, Goa, India
UCSC Xena funding source(s)
Supported by National Cancer Institute of the National Institutes of Health under award numbers 5U24CA180951-04 and 5U24CA210974-02.

UCSC Xena review

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Martin Abba

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Web
Beautiful app for data retrieval an visualization of different cancer genomics projects such as TCGA, ICGC, TARGET, etc. Also provide a set of analytic tools for survival analysis of selected features, correlation analysis, visualization of isoforms expression and mutation data.