Package: siggenes 1.81.0

Holger Schwender

siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

Authors:Holger Schwender

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

On BioConductor:siggenes-1.81.0(bioc 3.21)siggenes-1.80.0(bioc 3.20)

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

multiplecomparisonmicroarraygeneexpressionsnpexonarraydifferentialexpression

7.87 score 34 packages 74 scripts 4.9k downloads 72 mentions 51 exports 9 dependencies

Last updated 5 months agofrom:60ae98183a. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
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Exports:args.ebamargs.finda0args.samcat.ebamcat.statchisq.ebamchisq.statchisqClassd.statdensprebamebam2excelebam2htmlebamControlfind.a0findDeltafudge2fuzzy.ebamfuzzy.stathelp.ebamhelp.finda0help.samidentifylimma2ebamlimma2samlink.geneslink.siggeneslist.siggenesmd.plotna.handlingnclass.wandpi0.estplotplotArgumentsprintqvalue.calrowRanksWilcrowWilcoxonsamsam.plot2sam2excelsam2htmlsamControlshowsummarytrend.ebamtrend.statwilc.ebamwilc.statz.ebamz.find

Dependencies:BiobaseBiocGenericsgenericslatticeMASSMatrixmulttestscrimesurvival

siggenes Manual

Rendered fromsiggenes.Rnwusingutils::Sweaveon Mar 18 2025.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
EBAM Analysis for Categorical Datacat.ebam chisq.ebam
SAM Analysis for Categorical Datacat.stat chisq.stat
SAM Analysis Using a Modified t-statisticd.stat
Delta Plotsdelta.plot
Density Estimationdenspr
Empirical Bayes Analysis of Microarraysebam
Class EBAMEBAM EBAM-class plot,EBAM,ANY-method plot,EBAM-method print,EBAM-method show,EBAM-method summary,EBAM-method
Further EBAM ArgumentsebamControl find.a0Control
Computation of the Fudge Factorfind.a0
Class FindA0FindA0 FindA0-class plot,FindA0,ANY-method plot,FindA0-method print,FindA0-method show,FindA0-method
Finding the Threshold DeltafindDelta
Fudge Factorfudge2
EBAM and SAM for Fuzzy Genotype Callsfuzzy.ebam fuzzy.stat
Help files or argument list for EBAM-specific methodsargs.ebam help.ebam
Help files or argument list for FindA0-specific methodsargs.finda0 help.finda0
Help files or argument list for SAM-specific methodsargs.sam help.sam
limma to SAM or EBAMlimma2ebam limma2sam
Links for a list of geneslink.genes
Links for a SAM or an EBAM objectlink.siggenes
List of the significant geneslist.siggenes
MD Plotmd.plot
Number of cells in a histogramnclass.wand
Estimation of the prior probabilitypi0.est
Plot ArgumentsplotArguments
Plot ArgumentsplotFindArguments
Computation of the q-valueqvalue.cal
Rowwise Wilcoxon Rank Sum StatisticsrowRanksWilc rowWilcoxon
Significance Analysis of Microarraysam
Class SAMidentify,SAM-method plot,SAM,ANY-method plot,SAM-method print,SAM-method SAM SAM-class show,SAM-method summary,SAM-method
SAM Plotsam.plot2
Further SAM ArgumentssamControl
CSV file of a SAM or an EBAM objectebam2excel sam2excel siggenes2excel
HTML page for a SAM or an EBAM objectebam2html sam2html siggenes2html
Classes sumSAM and sumEBAMprint,sumEBAM-method print,sumSAM-method show,sumEBAM-method show,sumSAM-method sumEBAM-class sumSAM-class
EBAM Analysis of Linear Trendtrend.ebam trend.ebam.data.frame trend.ebam.default trend.ebam.list
SAM Analysis of Linear Trendtrend.stat trend.stat.data.frame trend.stat.default trend.stat.list
EBAM Analysis Using Wilcoxon Rank Statisticswilc.ebam
SAM Analysis Using Wilcoxon Rank Statisticswilc.stat
EBAM analysis Using t- or F-testz.ebam z.find