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DESCRIPTION
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Package: dsOmics
Type: Package
Title: DataSHIELD server site Omic functions
Version: 1.0.19
Date: 2024-11-04
Authors@R: c(person("Yannick", "Marcon", , "[email protected]", role = "aut"),
person("Xavier", "Esriba-Montagut", , "[email protected]", role = "aut"),
person("Juan R.", "Gonzalez", ,"[email protected]", role = c("aut", "cre")))
Description: DataSHIELD server site Omic functions.
Depends: R (>= 3.6.0),
resourcer,
tidyverse,
magrittr,
resourcer (>= 1.1.1)
Imports:
Biobase,
SNPRelate (>= 1.26.0),
GENESIS,
GWASTools,
GenomicRanges,
SummarizedExperiment,
MEAL (>= 1.22.0),
knitr,
DESeq2,
edgeR,
dplyr,
readr,
wkb,
Rcpp (>= 1.0.7)
AggregateMethods:
alleleFrequencyDS,
fastAlleleFrequencyDS,
exactHWEDS,
featureNamesDS,
varLabelsDS,
fvarLabelsDS,
featureDataDS,
nSamplesDS,
nFeaturesDS,
tablePhenoDS,
limmaDS2,
getVariable,
getChromosomeNamesDS,
GWASDS,
plinkDS,
DESeq2DS,
edgeRDS,
PCASNPSDS,
snptestDS,
genoDimensionsDS,
plotPCASNPSDS,
c=base::c,
fastGWAS_ColSums,
PCADS,
plotPCADS
AssignMethods:
selFeatureDS,
cellCountsDS,
GenotypeDataDS,
selSNPDS,
getSNPSbyGenDS,
addPhenoDataDS,
removeOutliersDS,
createRSEDS,
RNAseqPreprocDS,
PRSDS,
PRSDS_aux,
limmaDS,
make_valid_namesDS,
fastGWAS_S,
fastGWAS_getFitted.values,
fastGWAS_getResiduals,
fastGWAS_PHENO_removeNAindiv,
fastGWAS_S_means,
extractPhenoFromGDSDS,
subsetExpressionSetDS,
subsetExpressionSet2DS,
subsetGenoDS,
geno_pca_pooled_addPCDS,
geno_pca_pooled_addPC2GenoDS,
pDataDS,
methylation_array_convertDS
Options:
default.nfilter.diffP.epsilon=3,
default.nfilter.diffP.gamma=0.1,
default.nfilter.MAF=0.05,
nfilter.subset=3
License: MIT + file LICENSE
biocViews: DNAMethylation, Microarray, Software, WholeGenome, GWAS, Non-disclosive
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Encoding: UTF-8