rbamtools specifications

Information


Unique identifier OMICS_07008
Name rbamtools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM,BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.16.11
Stability Stable
Requirements
methods, xtable, refGenome(≥1.6.1)
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Wolfgang Kaisers

Publication for rbamtools

rbamtools citations

 (2)
library_books

Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data

2017
Int J Mol Sci
PMCID: 5618549
PMID: 28872584
DOI: 10.3390/ijms18091900

[…] 162.5×106 alignments from TopHat (for more details see ).The number of gap-sites present in single samples as well as in merged samples has been calculated using the framework provided by R packages rbamtools (version 2.16.0, available on CRAN), refGenome (version 1.7.3, available on CRAN), and spliceSites (version 1.23.3, available on Bioconductor). […]

library_books

Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p derived miRNA hairpin loop sequences

2014
Oncogene
PMCID: 4224628
PMID: 24909177
DOI: 10.1038/onc.2014.150

[…] black) and 3p (red) elements were depicted separately from miRNAs without these annotations (blue).To count the number of reads corresponding to each annotated miRNA component, we used the R package ‘rbamtools' version 2.0 to extract the mapping position of each read in the bam file that fell within an miRNA. To remove adapter sequence and to account for uncertainty in the annotation of the exact […]

rbamtools institution(s)
Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Dusseldorf, Dusseldorf, Germany; Institut fur Virologie, Heinrich Heine University Dusseldorf, Dusseldorf, Germany; Mathematical Institute, Heinrich Heine University Dusseldorf, Dusseldorf, Germany
rbamtools funding source(s)
Supported by the German Ministry of Research and Education (Network Gerontosys), DFG [SCHA 909/3-1], the Heinz Ansmann Foundation for AIDS Research, Dusseldorf, Germany, and the Jurgen Manchot Stiftung, and the Deutsche Forschungsgemeinschaft [SCHW 1508/3-1].

rbamtools reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review rbamtools