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Rnaseqmixture specifications

Information


Unique identifier OMICS_33517
Name Rnaseqmixture
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Matthew Ritchie

Publication for Rnaseqmixture

Rnaseqmixture citations

 (2)
library_books

Interferon signaling in ascites associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients

2017
BMC Genomics
PMCID: 5359932
PMID: 28327095
DOI: 10.1186/s12864-017-3630-9

[…] xons and corrected for contamination by tumor cells as described []. The source code for implementing the algorithm for TPM correction has also been deposited at GitHub (https://github.com/IMTMarburg/rnaseqmixture). Genes were considered expressed if they had a minimum TPM value of 3. TAM samples with TPM >50 for EPCAM or MSLN were excluded due to presumed tumor cell contamination. All genomic seq […]

library_books

A transcriptome based global map of signaling pathways in the ovarian cancer microenvironment associated with clinical outcome

2016
Genome Biol
PMCID: 4877997
PMID: 27215396
DOI: 10.1186/s13059-016-0956-6

[…] TCF7, TGFBR3.The source code for implementing our algorithm and the simulations described in the present study are included as Additional file and deposited at GitHib (https://github.com/IMTMarburg/rnaseqmixture) and Zonodo (doi:10.5281/zenodo.48872). […]


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Rnaseqmixture institution(s)
ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia; Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Statistics Department, George R. Brown School of Engineering, Rice University, Houston, TX, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University School of Medicine, Washington, DC, USA; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
Rnaseqmixture funding source(s)
Supported by the National Health and Medical Research Council [1050661, 1079756, 1045936, 1059622, 1104924 and 1058892]; Victorian State Government Operational Infrastructure Support, Australian Government NHMRC IRIISS and the Ian Potter Centre for Genomics and Personalised Medicine.

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