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Biostrings specifications

Information


Unique identifier OMICS_29386
Name Biostrings
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.48.0
Stability Stable
Requirements
methods, stats, graphics, utils, RUnit, BSgenome.Hsapiens.UCSC.hg18, S4Vectors(>=0.17.25), R(>=2.8.0), XVector(>=0.19.8), hgu95av2probe, hgu95av2cdf, BiocGenerics(>=0.15.6), IRanges(>=2.13.24), BSgenome(>=1.13.14), BSgenome.Celegans.UCSC.ce2(>=1.3.11), BSgenome.Dmelanogaster.UCSC.dm3(>=1.3.11), drosophila2probe, hgu133aprobe, GenomicFeatures(>=1.3.14), affy(>=1.41.3), affydata(>=1.11.5)
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Hervé Pagès

Additional information


http://bioconductor.org/packages/release/bioc/vignettes/Biostrings/inst/doc/BiostringsQuickOverview.pdf

Biostrings citations

 (138)
library_books

Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium

2018
PLoS One
PMCID: 5942774
PMID: 29742107
DOI: 10.1371/journal.pone.0195869

[…] he computation of CIB and all statistical analyses were carried out using the R statistical computing software V3.3.2. The kSamples package was used for the Anderson-Darling test and the Bioconductor Biostrings package was used to process DNA sequence data.Hierarchical clustering of CIB using average linkage was carried out by means of the TM4 MeV v4.9.0 stand-alone local client using the Pearson […]

library_books

Genome wide identification of the auxin response factor gene family in Cicer arietinum

2018
BMC Genomics
PMCID: 5921756
PMID: 29703137
DOI: 10.1186/s12864-018-4695-9

[…] SDS server. Gene duplications were determined using the PGDD database and the orthologous relationships were visualized using Circoletto. Amino acid content of the MR domain was calculated using the ‘Biostrings’ Bioconductor package. The putative cis-acting regulatory elements in the promoters were analyzed using custom Python scripts. In silico expression data were obtained via the NCBI EST datab […]

library_books

Cryptic glucocorticoid receptor binding sites pervade genomic NF κB response elements

2018
Nat Commun
PMCID: 5889392
PMID: 29626214
DOI: 10.1038/s41467-018-03780-1

[…] to contain an κBRE if their genomic sequences contained at least one site matching the NF-κB (Hsapiens-JASPAR_2014-NFKB1-MA0105.3) JASPAR motif with a score of 90% or greater, as determined using the Biostrings package in Bioconductor. For Gene Ontology analyses, the nearest transcription start site to each peak was determined with the ChIPpeakAnno package and results input to the DAVID ontology s […]

call_split

Prevalence and impact of baseline resistance associated substitutions on the efficacy of ledipasvir/sofosbuvir or simeprevir/sofosbuvir against GT1 HCV infection

2018
Sci Rep
PMCID: 5816647
PMID: 29453451
DOI: 10.1038/s41598-018-21303-2
call_split See protocol

[…] io.ncsu.edu/BioEdit/bioedit.html).Translation of codons, calculation of proportions of RASs, and linkage analysis of RASs were carried out using custom R scripts (https://www.r-project.org/) with the BioStrings package (http://bioconductor.org/packages/release/bioc/html/Biostrings.html). Amino acid substitutions at each position were identified by comparing translated consensus reads against HCV H […]

library_books

Disentangling the Causes for Faster X Evolution in Aphids

2018
Genome Biol Evol
PMCID: 5798017
PMID: 29360959
DOI: 10.1093/gbe/evy015

[…] s were performed with an R script. A reciprocal best hit criterion was used to identify putative orthologous genes between the two species. These were aligned by the pairWiseAlignment function of the Biostrings package (). Indels were inspected to flag CDS regions where the two species did not present the same reading frame. Bases in these regions were replaced with Ns, and were trimmed by the Gbl […]

library_books

Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random

2018
Genome Biol Evol
PMCID: 5786225
PMID: 29325123
DOI: 10.1093/gbe/evy005

[…] mean GC content were calculated for sliding windows of 4 kb using the rollapply function of the zoo package (). GC-content for sliding windows was calculated using the letterFrequency function of the Biostrings package (). Only methylated sites with an identification Phred score > 30 (99.9% probability of correct identification) were used in this study and summed up for the sliding window range. S […]

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