Package: PepSAVIms 0.9.2
Pritchard David
PepSAVIms: PepSAVI-MS Data Analysis
An implementation of the data processing and data analysis portion of the PepSAVI-MS pipeline developed by principal investigator Christine Kirkpatrick and the Hicks Laboratory at the University of North Carolina, as presented in the paper \emph{The "PepSAVI-MS" Pipeline for Natural Product Bioactive Peptide Discovery} (DOI:10.1021/acs.analchem.6b03625). The statistical analysis package presented herein provides a collection of software tools used to facilitate the prioritization of putative bioactive peptides from a complex biological matrix. Tools are provided to deconvolute mass spectrometry features into a single representation for each peptide charge state, filter compounds to include only those possibly contributing to the observed bioactivity, and prioritize these remaining compounds for those most likely contributing to each bioactivity data set.
Authors:
PepSAVIms_0.9.2.tar.gz
PepSAVIms_0.9.2.zip(r-4.5)PepSAVIms_0.9.2.zip(r-4.4)PepSAVIms_0.9.2.zip(r-4.3)
PepSAVIms_0.9.2.tgz(r-4.4-any)PepSAVIms_0.9.2.tgz(r-4.3-any)
PepSAVIms_0.9.2.tar.gz(r-4.5-noble)PepSAVIms_0.9.2.tar.gz(r-4.4-noble)
PepSAVIms_0.9.2.tgz(r-4.4-emscripten)PepSAVIms_0.9.2.tgz(r-4.3-emscripten)
PepSAVIms.pdf |PepSAVIms.html✨
PepSAVIms/json (API)
NEWS
# Install 'PepSAVIms' in R: |
install.packages('PepSAVIms', repos = c('https://dapritchard.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dpritchlibre/pepsavims/issues
Last updated 7 years agofrom:c37a0b2202. Checks:OK: 1 WARNING: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 21 2024 |
R-4.5-win | WARNING | Nov 21 2024 |
R-4.5-linux | WARNING | Nov 21 2024 |
R-4.4-win | WARNING | Nov 21 2024 |
R-4.4-mac | WARNING | Nov 21 2024 |
R-4.3-win | WARNING | Nov 21 2024 |
R-4.3-mac | WARNING | Nov 21 2024 |
Exports:binMSextract_rankedextractMSfilterMSmsDatrankEN
Dependencies:elasticnetlars
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Consolidate mass spectrometry observations | binMS |
Bioactivity data | bioact |
Extract candidate compounds | extract_ranked |
Extract embedded mass spectrometry data | extractMS |
Filter compounds from mass spectrometry data | filterMS |
Mass spectrometry data | mass_spec |
Constructor for class 'msDat' | msDat |
Basic information for class 'filterMS' | print.filterMS |
Print method for class 'msDat' | print.msDat |
Basic information for class 'rankEN' | print.rankEN |
Rank compounds via the Elastic Net path | rankEN |
Overview of the binning process | summary.binMS |
Overview of the filtering process | summary.filterMS |
Overview of the elastic net selection process | summary.rankEN |