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proBAMtools specifications

Information


Unique identifier OMICS_19081
Name proBAMtools
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.99.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Bing Zhang

Publication for proBAMtools

proBAMtools citations

 (2)
library_books

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

2018
Genome Biol
PMCID: 5793360
PMID: 29386051
DOI: 10.1186/s13059-017-1377-x

[…] ble to convert from mzIdentML and mzTab to proBed and bigBed. Analogously, several tools are available to write proBAM files, such as the Bioconductor proBAMr package. An additional R package, called proBAMtools, is also available to analyze fully exported MS-based proteomics results in proBAM []. proBAMtools was specifically designed to perform various analyses using proBAM files, including funct […]

library_books

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

2017
J Proteome Res
PMCID: 5715286
PMID: 28849660
DOI: 10.1021/acs.jproteome.7b00370

[…] //github.com/PRIDE-Toolsuite/PGConverter) write to proBed, proBAMr writes to proBAM, and proBAMconvert (http://probam.biobix.be) writes to both formats. PGConverter also contains a validation module. proBAMtools is available for further downstream analysis of proBAM files.A systematic approach to quality control (QC) is an essential requirement to have confidence in the results of a MS experiment, […]


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proBAMtools institution(s)
Department of Biomedical Informatics, Department of Biochemistry, Department of Cancer Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA; Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
proBAMtools funding source(s)
Supported by the National Institutes of Health grant U24CA159988.

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