Alevin

Alevin is a tool for estimating gene abundances in droplet-based single-cell dscRNA-seq data. The Alevin tool is included in the Salmon package (see links).

Topic

RNA-seq; Gene expression; Transcriptomics

Details

Operation: Sequence composition calculation; RNA-Seq quantification; Gene expression analysis
Software interface: Command-line user interface
Language: C++
Operating system: Linux
License: GNU General Public License v3

Cost

Version name: 1.0.0

Maturity:

Credit: The US National Science Foundation, the US National Institutes of Health, the Chan Zuckerberg Initiative DAF.
Contact: Rob Patro rob.patro _at_ cs.stonybrook.edu | Carl Kingsford carlk _at_ cs.cmu.edu
Collection: -

Publications

Srivastava A, Malik L, Smith T, Sudbery I, Patro R "Alevin efficiently estimates accurate gene abundances from dscRNA-seq data." Genome Biol. 2019 Mar 27;20(1):65. https://doi.org/10.1186/s13059-019-1670-y
PMID: 30917859
PMCID: PMC6437997

Download and documentation

Source: https://github.com/COMBINE-lab/salmon
Documentation: https://salmon.readthedocs.io/en/latest/
Home page: https://github.com/COMBINE-lab/salmon
Links: https://bioinformaticshome.com/tools/rna
-seq/descriptions/Salmon.html

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Alevin

Alevin

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