tximport protocols

tximport specifications

Information


Unique identifier OMICS_11762
Name tximport
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Charlotte Soneson <>

Publication for tximport

tximport IN pipeline

2017
PMCID: 5614841
PMID: 28805815
DOI: 10.1038/nn.4620

[…] strand-specific single-end rna-seq read files were analyzed to obtain transcript level counts using kallisto66, with the settings –rf-stranded -b 100. the counts were subsequently passed to the tximport r package to collapse to gene level counts. pairwise differential expression analysis between groups was then performed using edger with default settings67., using an adjusted p-value cutoff […]

tximport institution(s)
Institute for Molecular Life Sciences, University of Zurich, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
tximport funding source(s)
This work was supported by the “RNA & Disease” National Center of Competence in Research, an SNSF project grant (143883) by the European Commission through the 7th Framework Collaborative Project RADIANT (Grant Agreement Number: 305626), and by NIH grant 5T32CA009337-35.

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