https://github.com/bzhanglab/pepquery
PepQuery: a targeted peptide search engine
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.0%) to scientific vocabulary
Keywords
Repository
PepQuery: a targeted peptide search engine
Basic Info
- Host: GitHub
- Owner: bzhanglab
- License: gpl-3.0
- Language: Java
- Default Branch: master
- Homepage: http://pepquery.org
- Size: 321 KB
Statistics
- Stars: 4
- Watchers: 4
- Forks: 0
- Open Issues: 3
- Releases: 0
Topics
Metadata Files
README.md
PepQuery
PepQuery: a targeted peptide search engine for identifying or validating known and novel peptides of interest in MS-based proteomics data.
Web server: http://pepquery.org/
PepQuery can be used in two ways: 1. Online version: search a peptide of interest in curated large-scale proteomics MS/MS datasets; 2. Standalone version: batch search a list of peptides in any MS/MS datasets.
How to cite:
Wen, B., et al. (2019). "PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations." Genome research 29(3): 485-493. Manuscript
Wen, B., Li, K., Zhang, Y. et al. (2020). "Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis." Nature Communications 11, 1759. Manuscript
Wen, B., Zhang, B. (2023) PepQuery2 democratizes public MS proteomics data for rapid peptide searching. Nature Communications 14, 2213. Manuscript
Owner
- Name: Zhang Lab
- Login: bzhanglab
- Kind: organization
- Location: Houston, TX
- Website: https://www.zhang-lab.org
- Repositories: 15
- Profile: https://github.com/bzhanglab
Translating omics data into biological insights.
GitHub Events
Total
- Issues event: 30
- Watch event: 2
- Issue comment event: 68
- Fork event: 1
Last Year
- Issues event: 30
- Watch event: 2
- Issue comment event: 68
- Fork event: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 15
- Total pull requests: 0
- Average time to close issues: about 1 month
- Average time to close pull requests: N/A
- Total issue authors: 10
- Total pull request authors: 0
- Average comments per issue: 0.93
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 15
- Pull requests: 0
- Average time to close issues: about 1 month
- Average time to close pull requests: N/A
- Issue authors: 10
- Pull request authors: 0
- Average comments per issue: 0.93
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- anuC (7)
- treko90 (5)
- sophiachen1 (3)
- EmaEtch (2)
- bioyangyang (2)
- ofleitas (2)
- bszeitz (1)
- sarinita (1)
- feather-W (1)
- zxseason (1)
- colin986 (1)
- adajani (1)
- qqwang-berkeley (1)
- anu80125 (1)
- lindenb (1)
Pull Request Authors
- tretyacv (1)
- Seb-Leb (1)
- anuC (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- org.junit.jupiter:junit-jupiter-api 5.8.2 compile
- JFASTA:JFASTA 2.2.0
- com.alibaba:fastjson 1.2.83
- com.amazonaws:aws-java-sdk-s3 1.12.261
- com.compomics:utilities 5.0.39
- com.fasterxml.jackson.core:jackson-annotations 2.13.1
- com.github.chhh:msftbx 1.8.8
- com.github.dpaukov:combinatoricslib3 3.3.3
- com.google.guava:guava 31.0.1-jre
- commons-cli:commons-cli 1.5.0
- org.apache.commons:commons-lang3 3.12.0
- org.apache.commons:commons-math3 3.6.1
- org.apache.logging.log4j:log4j-api 2.17.2
- org.apache.logging.log4j:log4j-core 2.17.2
- org.apache.logging.log4j:log4j-slf4j-impl 2.17.2
- org.jgrapht:jgrapht-core 1.5.1
- org.tukaani:xz 1.9
- org.xerial:sqlite-jdbc 3.36.0.3
- uk.ac.ebi.pride.utilities:pride-mod 2.1.12
- org.junit.jupiter:junit-jupiter-engine 5.8.2 test