Package: HEM 1.79.0

HyungJun Cho

HEM: Heterogeneous error model for identification of differentially expressed genes under multiple conditions

This package fits heterogeneous error models for analysis of microarray data

Authors:HyungJun Cho <[email protected]> and Jae K. Lee <[email protected]>

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HEM.pdf |HEM.html✨
HEM/json (API)

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

Peer review:

Datasets:
  • mubcp - Gene expression data for mouse B cell development
  • pbrain - Gene expression data for primate brains

On BioConductor:HEM-1.77.0(bioc 3.20)HEM-1.76.0(bioc 3.19)

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

microarraydifferentialexpression

4.30 score 6 scripts 267 downloads 27 mentions 27 exports 2 dependencies

Last updated 23 days agofrom:47fa135fcb. Checks:OK: 1 NOTE: 4 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 30 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 30 2024
R-4.4-mac-x86_64WARNINGOct 30 2024
R-4.4-mac-aarch64WARNINGOct 30 2024
R-4.3-win-x86_64NOTEOct 30 2024
R-4.3-mac-x86_64WARNINGOct 30 2024
R-4.3-mac-aarch64WARNINGOct 30 2024

Exports:am.tranam.tran.halfbase.ASE.Oligbase.error.Oligbase.error.Olig.quanOnlybase.PSE.Oligboot.base.ASE.Oligboot.base.error.Oligboot.base.PSE.Oligfixbound.predict.smooth.splinehemhem.eb.priorhem.fdrhem.null.nohem.null.onehem.null.twohem.preprocnonpar.error.Olignonpar.no.error.Olignonpar.rep.error.Oligpar.error.Oligpar.no.error.Oligpar.rep.error.Oligpermutquant.normalquant.normal2remove.sig.genes

Dependencies:BiobaseBiocGenerics

HEM Overview

Rendered fromHEM.Rnwusingutils::Sweaveon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
AM transformation for LPEam.tran
AM transformation for LPEam.tran.half
Baseline ASE estimation for oligonucleotide arraysbase.ASE.Olig
Baseline error estimation for oligonucleotide arraysbase.error.Olig
Baseline error estimation for oligonucleotide arraysbase.error.Olig.quanOnly
Baseline PSE estimation for oligonucleotide arraysbase.PSE.Olig
Baseline error bootstrap estimation for oligonucleotide arraysboot.base.ASE.Olig
Baseline error bootstrap estimation for oligonucleotide arraysboot.base.error.Olig
Baseline error bootstrap estimation for oligonucleotide arraysboot.base.PSE.Olig
Prediction using smoothing spinefixbound.predict.smooth.spline
Heterogeneous Error Model for Identification of Differential Expressed Genes Under Multiple Conditionshem
Empirical Bayes (EB) Prior Specificationhem.eb.prior
FDR Evaluationhem.fdr
Generation of null datahem.null.no
Generation of null datahem.null.one
Generation of null datahem.null.two
Preprocessinghem.preproc
Gene expression data for mouse B cell developmentmubcp
Baseline error nonparametric estimation for oligonucleotide arraysnonpar.error.Olig
Baseline error nonparametric estimation for oligonucleotide arraysnonpar.no.error.Olig
Baseline error nonparametric estimation for oligonucleotide arraysnonpar.rep.error.Olig
Baseline error parametric estimation for oligonucleotide arrayspar.error.Olig
Baseline error parametric estimation for oligonucleotide arrayspar.no.error.Olig
Baseline error parametric estimation for oligonucleotide arrayspar.rep.error.Olig
Gene expression data for primate brainspbrain
Permutationpermut
Quantile normalizationquant.norm
Normalizationquant.normal
Normalizationquant.normal2
Quantile normalizationquant.normalize
Remove significant genesremove.sig.genes