Package: ELMER 2.37.0

Tiago Chedraoui Silva

ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Authors:Tiago Chedraoui Silva [aut, cre], Lijing Yao [aut], Simon Coetzee [aut], Nicole Gull [ctb], Hui Shen [ctb], Peter Laird [ctb], Peggy Farnham [aut], Dechen Li [ctb], Benjamin Berman [aut]

ELMER_2.37.0.tar.gz
ELMER_2.37.0.zip(r-4.7)ELMER_2.37.0.zip(r-4.6)ELMER_2.37.0.zip(r-4.5)
ELMER_2.37.0.tgz(r-4.6-any)ELMER_2.37.0.tgz(r-4.5-any)
ELMER_2.37.0.tar.gz(r-4.7-any)ELMER_2.37.0.tar.gz(r-4.6-any)
ELMER_2.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ELMER/json (API)
NEWS

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

On BioConductor:ELMER-2.37.0(bioc 3.24)ELMER-2.35.1(bioc 3.23)

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

dnamethylationgeneexpressionmotifannotationsoftwaregeneregulationtranscriptionnetwork

5.55 score 179 scripts 545 downloads 19 mentions 38 exports 211 dependencies

Last updated from:b7f87eaa43. Checks:9 ERROR, 1 OK. Indexed: yes.

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linux-release-x86_64ERROR801
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wasm-releaseOK233

Exports:addDistNearestTSScalculateEnrichementcreateBigWigDNAmetArraycreateIGVtrackcreateMAEcreateMotifRelevantTfscreateTSVTemplatesget.diff.methget.enriched.motifget.feature.probeget.pairget.permuget.TFsgetExpgetExpSamplesgetGeneIDgetMetgetMetSamplesGetNearGenesgetRandomPairsgetRegionNearGenesgetSymbolgetTCGAgetTFBindingSitesgetTFtargetsgetTSSheatmapGeneheatmapPairsmetBoxPlotmotif.enrichment.plotpreAssociationProbeFilteringpromoterMethrender_reportscatter.plotschematic.plotTCGA.pipeTF.rank.plotTFsurvival.plot

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbootbroomBSgenomebslibcachemcarcarDatacheckmatecigarillocirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirDerivdichromatdigestdoBydoParalleldownloaderdplyrELMER.dataensembldbevaluatefarverfastmapfilelockfontawesomeforeachforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentnlmenloptrnnetnumDerivopensslotelpbkrtestpillarpkgconfigplotlyplyrpngpolynomprettyunitsprogresspromisesProtGenericspurrrquantregR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreformulasreshapereshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstatixrstudioapirtracklayerrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfoshapesnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsysTCGAbiolinksTCGAbiolinksGUI.datatibbletidyrtidyselecttimeDatetinytextzdbUCSC.utilsurcautf8VariantAnnotationvctrsviridisLitevroomwithrxfunXMLxml2XVectoryamlzoo

Readme and manuals

Help Manual

Help pageTopics
Calculate the distance between probe and gene TSSaddDistNearestTSS
Adds mutation information to MAEaddMutCol
Calculate distance from region to nearest TSScalcDistNearestTSS
Calculate motif ErichmentcalculateEnrichement
Create a bigwig file for IGV visualization of DNA methylation data (Array)createBigWigDNAmetArray
Create a junction track for IGV visualization of interectioncreateIGVtrack
Construct a Multi Assay Experiment for ELMER analysiscreateMAE
Get family of transcription factorscreateMotifRelevantTfs
Create summary document for TCGA.pipe functioncreateSummaryDocument
Create examples files for Sample mapping and information used in createMAE functioncreateTSVTemplates
ELMER (Enhancer Linking by Methylation/Expression Relationships)ELMER
Use Hocomoco motif and homer to identify motifs in a given regionfindMotifRegion
Identify hypo/hyper-methylated CpG sites between two groups (i.e. normal vs tumor samples, treated vs untreated).get.diff.meth
get.enriched.motif to identify the overrepresented motifs in a set of probes (HM450K) regions.get.enriched.motif
get.feature.probe to select probes within promoter regions or distal regions.get.feature.probe
get.pair to predict enhancer-gene linkages.get.pair
get.permu to generate permutation results for calculation of empirical P values for each enhancer-gene linkage.get.permu
Calculate empirical PvalueGet.Pvalue.p
summarize MR TF as a binary table with 1 if TF was found in the analysis, 0 if notget.tab
Creating matrix for MR TF heatmapget.tabs
get.TFs to identify regulatory TFs.get.TFs
get450K to download HM40K DNA methylation data for certain cancer types from TCGA website. @description get450K is a function to download latest version of HM450K DNA methylation for all samples of certain cancer types from GDC website.get450K
getClinic to download clinic data for certain cancer types from TCGA website.getClinic
Get Gene expression object from MAEgetExp
Get Gene expression object samples from MAEgetExpSamples
getGeneID to report gene id from symbolgetGeneID
Get DNA methylation object from MAEgetMet
Get DNA methylation object samples from MAEgetMetSamples
GetNearGenes to collect nearby genes for one locus.GetNearGenes
Get random pairsgetRandomPairs
Identifies nearest genes to a regiongetRegionNearGenes
getRNAseq to download all RNAseq data for a certain cancer type from TCGA.getRNAseq
getSymbol to report gene symbol from idgetSymbol
getTCGA to download DNA methylation, RNA expression and clinic data for all samples of certain cancer type from TCGA.getTCGA
Get human TF list from the UNiprot databasegetTF
Get MR TF binding regions infered by ELMERgetTFBindingSites
Get TF target genesgetTFtargets
getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated.getTSS
Heatmap for correlation between probes DNA methylation and a single gene expression.heatmapGene
Heatmap of pairs gene and probes anti-correlatedheatmapPairs
lable linear regression formulalm_eqn
scatter.plot to plot scatter plots between gene expression and DNA methylation.metBoxPlot
motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORsmotif.enrichment.plot
Filtering probespreAssociationProbeFiltering
promoterMeth to calculate associations of gene expression with DNA methylation at promoter regionspromoterMeth
Build report for TCGA.pipe functionrender_report
scatterscatter
scatter.plot to plot scatter plots between gene expression and DNA methylation.scatter.plot
schematic.plot to plot schematic plots showing the locations of genes and probes.schematic.plot
Stat.diff.methStat.diff.meth
U test (non parameter test) for permutation. This is one probe vs nearby gene which is good for computing each probes for nearby genes.Stat.nonpara
Stat.nonpara.permuStat.nonpara.permu
Make MR TF binary tablesummarizeTF
ELMER analysis pipeline for TCGA data.TCGA.pipe
TF.rank.plot to plot the scores (-log10(P value)) which assess the correlation between TF expression and average DNA methylation at motif sites.TF.rank.plot
Creates survival plot of based on the expression of a TFTFsurvival.plot