Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: customProDB

https://packages.ecosyste.ms/registries/bioconductor.org/packages/customProDB

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
1 version
Latest release: about 1 year ago
24,485 downloads total

Papers Mentioning customProDB 7

10.1186/s40478-018-0548-7

Proteomic analysis of Medulloblastoma reveals functional biology with translational potential
Cited by: 35
Author(s): Samuel Rivero-Hinojosa, Ling San Lau, Mojca Stampar, Jerome A. Staal, Huizhen Zhang, Heather Gordish‐Dressman, Paul A. Northcott, Stefan M. Pfister, Michael D. Taylor, Kristy J. Brown, Brian R. Rood
Software Mentions: 10
Published: over 6 years ago

10.15252/msb.20188503

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
Cited by: 479
Author(s): Dongxue Wang, Basak Eraslan, Thomas Wieland, Björn M. Hallström, Thomas A. Hopf, Daniel Paul Zolg, Jana Zecha, Anna Asplund, Lihua Li, Chen Meng, Martin Frejno, Tobias Schmidt, Karsten Schnatbaum, Mathias Wilhelm, Fredrik Pontén, Mathias Uhlén, Julien Gagneur, Hannes Hahne, Bernhard Küster
Software Mentions: 8
Published: almost 6 years ago

10.1016/j.celrep.2019.11.026

Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome
Cited by: 53
Author(s): Edward Lau, Yu Han, Damon R. Williams, Cody T Thomas, Rajani Shrestha, Joseph C. Wu, Maggie Lam
Software Mentions: 6
Published: almost 5 years ago

10.1074/mcp.RA118.000832

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets
Cited by: 17
Author(s): Zhe Ren, Da Qi, Nina Pugh, Kai Li, Bo Wen, Ruo Zhou, Shaohang Xu, Siqi Liu, Andrew R. Jones
Software Mentions: 5
Published: almost 6 years ago

10.1074/mcp.M115.052860

proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data
Cited by: 23
Author(s): Xiaojing Wang, Robbert J.C. Slebos, Matthew Chambers, David L. Tabb, Daniel C. Liebler, Bing Zhang
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-016-1133-3

PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq
Cited by: 50
Author(s): Bo Wen, Shaohang Xu, Ruo Zhou, Bing Zhang, Xiaojing Wang, Xin Liu, Xun Xu, Siqi Liu
Software Mentions: 2
Published: over 8 years ago

10.1038/sdata.2015.22

Proteomic analysis of colon and rectal carcinoma using standard and customized databases
Cited by: 21
Author(s): Robbert J.C. Slebos, Xia Wang, Xiaojing Wang, Bing Zhang, David L. Tabb, Daniel C. Liebler
Software Mentions: 2
Published: over 9 years ago