Package: SIGN 0.1.0

SIGN: Similarity Identification in Gene Expression

Provides a classification framework to use expression patterns of pathways as features to identify similarity between biological samples. It provides a new measure for quantifying similarity between expression patterns of pathways.

Authors:Seyed Ali Madani Tonekaboni [aut], Gangesh Beri [aut], Janosch Ortmann [aut], Benjamin Haibe-Kains [aut, cre]

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manual.pdf |manual.html✨
card.svg |card.png
SIGN/json (API)

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

On CRAN:

Conda:

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

geneexpressionclassificationclusteringsurvival

2.70 score 6 scripts 188 downloads 57 mentions 1 exports 131 dependencies

Last updated from:93c1e62eb5. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE364
source / vignettesOK264
linux-release-x86_64NOTE341
macos-release-arm64NOTE425
macos-oldrel-arm64NOTE223
windows-develNOTE325
windows-releaseNOTE262
windows-oldrelNOTE286
wasm-releaseOK164

Exports:TSC

Dependencies:abindannotateAnnotationDbiaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelBiocSingularBiostringsbitbit64blobbootstrapcachemclassclicodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdiagramdigestdir.expirydplyrfarverfastmapfilelockformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggplot2globalsgluegraphGSEABaseGSVAgtableh5mreadHDF5Arrayhttrhttr2ipredIRangesirlbaisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelavalifecyclelistenvmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisememusemimennetnumDerivopensslparallellypillarpkgconfigpngprodlimprogressrpurrrR6rappdirsRColorBrewerRcpprhdf5rhdf5filtersRhdf5librjsonrlangrmetarpartRSQLitersvdS4ArraysS4VectorsS7ScaledMatrixscalesSeqinfoshapeSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentSQUAREMstringistringrSummarizedExperimentSuppDistssurvcompsurvivalsurvivalROCsystibbletidyrtidyselectutf8vctrsviridisLitewithrXMLxtableXVector

Readme and manuals

Help Manual

Help pageTopics
BubbleSort is a function for calculating bubble sort correlation between two vectorsBubbleSort
EventRenaming is a function for changing annotation of censored samples to 0 and dead samples to 1 for survival analysisEventRenaming
ExpPhen_Matching is a function for matching samples between expression matrices and metadata matrix (clinical feature matrix)ExpPhen_Matching
ExpPhen_Subdividing is a function for grouping samples based on a clinical feature available in metadata matrix (clinical feature matrix)ExpPhen_Subdividing
ExpPheno_Categorize is a function for grouping samples based on their survival to 3 groups of poor, good, and intermediateExpPheno_Categorize
GeneMatching is a function to remove uncommon genes between a list of expression matricesGeneMatching
Genes_SimCal is a function to calculate similarity between a set of samples and 2 reference groups of samplesGenes_SimCal
GSVA_Calculation is a function for Calculating correlation between expression level of pathways between 2 groups using GSVAGSVA_Calculation
Pathway_Grouping is a function to make a pathway list from files containing genes within each pathwayPathway_Grouping
Pathway_similarity is a function for calculating correlation between expression level of pathways between 2 groups using all the available approaches in SIGNPathway_similarity
SIGN_Aggregate is a function to reshape the list of pathway scoring, time to death, and event and return a summary listSIGN_Aggregate
SIGN_Ensemble_SimCal is a function for Generating list fo similarities based on different pathway quantification methods and similarity measuresSIGN_Ensemble_SimCal
Similarities_Wrapper is wrapper to identify similarities between the expression of genes in target sample and the reference expression matrixSimilarities_Wrapper
SimSummary_2Class is a function to calculating similarity between two set of samplesSimSummary_2Class
Survival_Stats is a function for building cox model using all the features and each feature as a separate modelSurvival_Stats
SurvivalStat_PostProcess is a function to Extract summary statistics of the built cox modelSurvivalStat_PostProcess
TSC is a function to calculate transcriprtional similarity coefficient between two biological pathwaysTSC