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


No version available

Documentation


Maintainer


  • person_outline Daniel Jones

Publication for seqbias

seqbias citations

 (2)
library_books

Cyanophage encoded lipid desaturases: oceanic distribution, diversity and function

2017
PMCID: 5776448
PMID: 29028002
DOI: 10.1038/ismej.2017.159

[…] the 399 metagenomes from the Tara Oceans microbial, giant viruses and viral fractions with Salmon in the quasimapping mode with the following parameters ‘—meta —incompatPrior 0.0 —libType A —gcBias —seqBias —numBootstraps 100’. Quantification results were processed by tximport (version 1.4.0) (), followed by the filtering of sequences with <20 mapped reads and normalization with edgeR (version 3. […]

library_books

Sequence specific bias correction for RNA seq data using recurrent neural networks

2017
BMC Genomics
PMCID: 5310274
PMID: 28198674
DOI: 10.1186/s12864-016-3262-5

[…] unted 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 i […]

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.

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