Package: iq 1.9.12
Thang Pham
iq: Protein Quantification in Mass Spectrometry-Based Proteomics
An implementation of the MaxLFQ algorithm by Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160). In general, the tool can be used to integrate multiple proportional observations into a single quantitative value.
Authors:
iq_1.9.12.tar.gz
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iq.pdf |iq.html✨
iq/json (API)
NEWS
| # Install 'iq' in R: |
| install.packages('iq', repos = c('https://tvpham.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tvpham/iq/issues
- spikeins - An example dataset of 12 spike-in proteins
Last updated 11 months agofrom:2c9b407fad. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 04 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 04 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 04 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 04 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 04 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 04 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 04 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 04 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 04 2024 |
Exports:create_protein_listcreate_protein_tableextract_annotationfast_MaxLFQfast_preprocessfast_readmaxLFQmeanIntmedian_polishplot_proteinpreprocessprocess_long_formatprocess_wide_formattopN
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Creating a list of matrices of fragment ion intensities for all proteins | create_protein_list |
| Protein quantification for a list of proteins | create_protein_table |
| Protein annotation extraction | extract_annotation |
| The MaxLFQ algorithm | fast_MaxLFQ |
| Data filtering and normalization | fast_preprocess |
| Reading data from an input file | fast_read |
| The MaxLFQ algorithm for protein quantification | maxLFQ |
| The meanInt algorithm for protein quantification | meanInt |
| A wrapper for the R implementation of the median polish algorithm | median_polish |
| Plotting the underlying quantitative data for a protein | plot_protein |
| Data preprocessing for protein quantification | preprocess |
| Long format to a wide format table using the MaxLFQ algorithm | process_long_format |
| Merging rows with identical values in a particular column in a table | process_wide_format |
| An example dataset of 12 spike-in proteins | spikeins |
| The topN algorithm for protein quantification | topN |