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|Interface||Command line interface|
|Restrictions to use||None|
|License||Apache License version 2.0|
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- person_outline Juan Antonio Vizcaíno
Publication for ms-data-core-api
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
[…] and proBed, although it should be noted that the representation for proteogenomics data in mzIdentML has only been formalized recently . In this context, first of all, the open-source Java library ms-data-core-api, created to handle different proteomics file formats using the same interface, can be used to write proBed . A Java command line tool, PGConverter (https://github.com/PRIDE-Toolsuit […]
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
[…] s, can be used to manipulate them. To convert existing MS-based proteomics identifications results in mzIdentML and mzTab format, among other formats, several tools have also recently been developed. ms-data-core-api and PGConverter (https://github.com/PRIDE-Toolsuite/PGConverter) write to proBed, proBAMr writes to proBAM, and proBAMconvert (http://probam.biobix.be) writes to both formats. PGConve […]
Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes
[…] pective genomic coordinates and color coded for the type of modification.A separate FileConverter implemented in java supports standardized PSI file formats such as mzIdentML and mzTab through use of ms-data-core-api. () Furthermore, the file converter is integrated into a java implemented graphical user interface (GUI) for PoGo enabling non-bioinformaticians to map peptides to reference genomes. […]
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