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https://github.com/bmascat/lfq-proteomics-pipeline
All code, bash scrypts and pipelines used to analyse and visualise proteomic data from my experiments with my first Crispr KO model.
https://github.com/bmascat/lfq-proteomics-pipeline
bioinformatics goterm over-representation-analysis proteomics proteomics-data-analysis
Last synced: 28 days ago
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All code, bash scrypts and pipelines used to analyse and visualise proteomic data from my experiments with my first Crispr KO model.
- Host: GitHub
- URL: https://github.com/bmascat/lfq-proteomics-pipeline
- Owner: bmascat
- License: mit
- Created: 2020-08-23T13:19:50.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2022-08-21T13:30:30.000Z (over 2 years ago)
- Last Synced: 2024-11-08T17:56:23.046Z (about 1 month ago)
- Topics: bioinformatics, goterm, over-representation-analysis, proteomics, proteomics-data-analysis
- Language: R
- Homepage:
- Size: 42 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Proteomic analysis of CRISPR Hela KO Alms1 after TGF-B stimulation
All code and pipelines used to analyze and visualize proteomic data from my experiments with my first Crispr KO model
Differenticial expression analysis was performed with DEP package:
>Zhang X, Smits A, van Tilburg G, Ovaa H, Huber W, Vermeulen M (2018). “Proteome-wide identification of ubiquitin interactions using UbIA-MS.” Nature Protocols, 13, 530–550.
Go-Terms analysis and data results visualizations was performed with Clusterprofiler and GOplot packages to R:
>Yu G, Wang L, Han Y, He Q (2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), 284-287. doi: 10.1089/omi.2011.0118.
>Walter, Wencke, Fátima Sánchez-Cabo, and Mercedes Ricote. "GOplot: an R package for visually combining expression data with functional analysis." Bioinformatics (2015): btv300.