Package: messina 1.43.0

Mark Pinese

messina: Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems

Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.

Authors:Mark Pinese [aut], Mark Pinese [cre], Mark Pinese [cph]

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messina.pdf |messina.html✨
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NEWS

# Install 'messina' in R:
install.packages('messina', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • kirc.exprs - Example TCGA KIRC RNAseq expression and survival data
  • kirc.surv - Example TCGA KIRC RNAseq expression and survival data

On BioConductor:messina-1.43.0(bioc 3.21)messina-1.42.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressiondifferentialexpressionbiomedicalinformaticsclassificationsurvivalcpp

3.30 score 1 scripts 235 downloads 6 exports 34 dependencies

Last updated 2 months agofrom:c06bc28089. Checks:OK: 1 NOTE: 5 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-win-x86_64WARNINGDec 19 2024
R-4.5-linux-x86_64NOTEDec 19 2024
R-4.4-win-x86_64WARNINGDec 19 2024
R-4.4-mac-x86_64NOTEDec 19 2024
R-4.4-mac-aarch64NOTEDec 19 2024
R-4.3-win-x86_64WARNINGDec 19 2024
R-4.3-mac-x86_64NOTEDec 19 2024
R-4.3-mac-aarch64NOTEDec 19 2024

Exports:messinamessinaDEmessinaSurvmessinaTopResultsplotshow

Dependencies:clicodetoolscolorspacefansifarverforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcpprlangscalessurvivaltibbleutf8vctrsviridisLitewithr

Using Messina

Rendered frommessina.Rnwusingknitr::knitron Dec 19 2024.

Last update: 2014-03-21
Started: 2014-03-21

Readme and manuals

Help Manual

Help pageTopics
The Messina package for classification and outlier differential expression.messina-package
Find optimal single feature classifiersmessina
Detect differential expression in the presence of outliersmessinaDE
The MessinaFits classMessinaFits-class
The MessinaParameters classMessinaParameters-class
The MessinaResult classMessinaClassResult-class MessinaResult-class MessinaSurvResult-class
Find optimal prognostic features using the Messina algorithmmessinaSurv
Display a summary of the top results from a Messina analysismessinaTopResults
Plot the results of a Messina analysis on a classification / differential expression problem.plot,MessinaClassResult,missing-method plot,MessinaClassResult-method
Plot the results of a Messina analysis on a survival problem.plot,MessinaSurvResult,missing-method plot,MessinaSurvResult-method
Generic show methods for Messina objects.show,MessinaFits-method show,MessinaParameters-method show,MessinaResult-method
Example TCGA KIRC RNAseq expression and survival datakirc.exprs kirc.surv tcga_kirc_example