awesome-proteomics
An awesome list of proteomics tools and resources
https://github.com/lyons89/awesome-proteomics
Last synced: 7 days ago
JSON representation
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7. Protein Pathway Enrichment
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Table of Contents
- fgsea - R - fast gene set enrichment analysis - [paper](https://www.biorxiv.org/content/10.1101/060012v2.full)
- pathfindR - R - active subnetwork oriented pathway enrichment analyses that uses protein-protein ineteraction networks to enchance the standard pathway analysis method - [paper](https://www.frontiersin.org/articles/10.3389/fgene.2019.00858/full)
- phosphoRWHN - R - pathway enrichment for phosphoproteomics data - [paper](https://pubs.acs.org/doi/10.1021/acs.jproteome.1c00150)
- leapR - R - package for multiple pathway analysis - [paper](https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00963)
- fgsea - R - fast gene set enrichment analysis - [paper](https://www.biorxiv.org/content/10.1101/060012v2.full)
- leapR - R - package for multiple pathway analysis - [paper](https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00963)
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8. Kinase Motif/Activity Analysis
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Table of Contents
- KSEAapp - R - Kinase substrate enrichment analysis. I would recommend using with a freshly downloaded kinase-substarte database from phosphositeplus - [paper](https://pubmed.ncbi.nlm.nih.gov/28655153/)
- rnotifx - R - motif enrichment analyssis of PTMs on proteins, probably mostly used for phosphorylation - [paper](https://pubmed.ncbi.nlm.nih.gov/26572964/)
- KSEAapp - R - Kinase substrate enrichment analysis. I would recommend using with a freshly downloaded kinase-substarte database from phosphositeplus - [paper](https://pubmed.ncbi.nlm.nih.gov/28655153/)
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9. Top down data analysis
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Table of Contents
- ClipsMS - python - analysis of terminal and internal fragments in top-down mass spectrometry data - [paper](https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00952)
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Miscellaneous
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Table of Contents
- cytoscape - visualizing protein-protein interaction netweorks
- ProteoWizard - Great software for converting one MS file type to another. I mostly use it ot convert thermo .raw files to mzML - [paper](https://www.nature.com/articles/nbt.2377)
- IPSC - Interactive Peptide Spectrum Annotator, web based utility for shotgun mass spectrum annotation - [paper](https://www.mcponline.org/article/S1535-9476(20)32771-7/fulltext)
- PeCorA - R - peptide correlation analysis - [paper](https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00602)
- ProteaseGuru - C# - tool for In Silico Database Digestion, optimize bottom up experiments - [paper](https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00954)
- DeepLC - python - predicts retention times for peptides that have unseen modifications - [paper](https://www.nature.com/articles/s41592-021-01301-5)
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Programming Languages
Categories
1A. Leaning Resources - Proteomics
119
1. Leaning Resources
23
5. Raw Data Analysis
13
2. Databases
12
4. Assorted pipeline Tools
10
7. Protein Pathway Enrichment
7
6. Stastical Analysis
7
3. Raw data search software/algorithms
7
Miscellaneous
6
1B. Learning Resources - Programming
6
8. Kinase Motif/Activity Analysis
3
10. Multi-Omics data analysis
2
9. Top down data analysis
1
Sub Categories
Keywords
proteomics
8
mass-spectrometry
7
bioinformatics
4
r
4
python
3
proteomics-data
3
machine-learning
2
tmt
2
orbitrap-ms
2
fast
2
multiplatform
2
rpackage
2
protein-inference
1
protein-identification
1
comet
1
pathway-enrichment-analysis
1
subnetwork
1
label-free-quantification
1
isobaric-quantification
1
gui
1
data-independent-acquisition
1
data-dependent-acquisition
1
command-line-interface
1
deep-learning
1
peptide-modification
1
matrices
1
mathematics
1
linear-algebra
1
calculus
1
algebra
1
tutorial
1
peptides
1
bioconda
1
retention-time
1
msstats
1
labeling
1
visualization
1
tmt-data-analysis
1
orbitrap
1
limma
1
quantitative-proteomic-analysis
1
active-subnetworks
1
mass-spectrometry-data
1
csharp-code
1
visualisation
1
bioconductor
1
percolator
1
peptide-detection
1
conda
1
enrichment
1