seqbias specifications

Information


Unique identifier OMICS_01237
Name seqbias
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.8.0
Stability Stable
Requirements
methods, Rsamtools, zlibbioc, ggplot2, R(>=2.13.0), GenomicRanges(>=0.1.0), Biostrings(>=2.15.0)
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Daniel Jones <>

Publication for seqbias

seqbias in publications

 (2)
PMCID: 5310274
PMID: 28198674
DOI: 10.1186/s12864-016-3262-5

[…] the uniquely mapped reads at each position for all exonic regions and sampled sets of foreground and background sequences for our training rnn models using the sequence sampling function in the seqbias (1.20.0) package. it will be noted that we used the seqbias function to ensure that subsequent comparisons of our method to alternatives are fair. however, we can use our own sampling method […]

PMCID: 5690287
PMID: 29144233
DOI: 10.7554/eLife.30860.051

[…] http://zfin.org/; 23 jan 2017., transcript level counts were produced using salmon () in quasi-mapping-based mode with the new ensembl e90 transcripts as a reference (v0.8.2, options: --threads 4 --seqbias --gcbias --libtype isr). differentially spliced genes and differentially expressed transcripts were called using the r package masigpro (; ) after removing the 20% of genes with the lowest […]


To access a full list of publications, you will need to upgrade to our premium service.

seqbias institution(s)
Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Microbiology, University of Washington, Seattle, WA, USA
seqbias funding source(s)
Supported by Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272200800060C and by the Public Health Service grant (P51RR000166) from the National Institutes of Health.

seqbias reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review seqbias