Package: ELMER 2.31.0

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]

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NEWS

# Install 'ELMER' in R:

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

On BioConductor:ELMER-2.31.0(bioc 3.21)ELMER-2.30.0(bioc 3.20)

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

dnamethylation geneexpression motifannotation software generegulation transcription network

7.36 score 154 scripts 380 downloads 19 mentions 38 exports 203 dependencies

Last updated 2 months agofrom:1f888937c1. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:addDistNearestTSS calculateEnrichement createBigWigDNAmetArray createIGVtrack createMAE createMotifRelevantTfs createTSVTemplates get.diff.meth get.enriched.motif get.feature.probe get.pair get.permu get.TFs getExp getExpSamples getGeneID getMet getMetSamples GetNearGenes getRandomPairs getRegionNearGenes getSymbol getTCGA getTFBindingSites getTFtargets getTSS heatmapGene heatmapPairs metBoxPlot motif.enrichment.plot preAssociationProbeFiltering promoterMeth render_report scatter.plot schematic.plot TCGA.pipe TF.rank.plot TFsurvival.plot

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob boot broom BSgenome bslib cachem car carData checkmate circlize cli clipr clue cluster codetools colorspace ComplexHeatmap corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir Deriv dichromat digest doBy doParallel downloader dplyr ELMER.data ensembldb evaluate fansi farver fastmap filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 ggpubr ggrepel ggsci ggsignif GlobalOptions glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle lme4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr MultiAssayExperiment munsell nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig plogr plotly plyr png polynom prettyunits progress promises ProtGenerics purrr quantreg R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr reshape reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstatix rstudioapi rtracklayer rvest S4Arrays S4Vectors sass scales selectr shape snow SparseArray SparseM stringi stringr SummarizedExperiment survival sys TCGAbiolinks TCGAbiolinksGUI.data tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 XVector yaml zlibbioc

ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

Tiago Chedraoui Silva [aut], Lijing Yao [aut], Simon Coetzee [aut], Nicole Gull [ctb], Houtan Noushmehr [ctb], Dennis J. Hazelett [ctb], Peggy Farnham [aut], Hui Shen [ctb], Peter Laird [ctb], De-Chen Lin[ctb], Benjamin P. Berman [aut]

Rendered fromindex.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2018-11-20
Started: 2017-07-17

11 - ELMER: Use case

Rendered fromusecase.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2021-08-23
Started: 2018-03-25

2 - Introduction: Input data

Rendered frominput.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-04-06
Started: 2017-07-17

3.1 - Data input - Creating MAE object

Rendered fromanalysis_data_input.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2021-08-02
Started: 2017-07-17

3.2 - Identifying differentially methylated probes

Rendered fromanalysis_diff_meth.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-05-07
Started: 2017-07-17

3.3 - Identifying putative probe-gene pairs

Rendered fromanalysis_get_pair.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-05-07
Started: 2017-07-17

3.4 - Motif enrichment analysis on the selected probes

Rendered fromanalysis_motif_enrichment.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-05-07
Started: 2017-07-17

3.5 - Identifying regulatory TFs

Rendered fromanalysis_regulatory_tf.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-05-07
Started: 2017-07-19

3.6 - TCGA.pipe: Running ELMER for TCGA data in a compact way

Rendered frompipe.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2020-04-14
Started: 2017-07-17

4.1 - Scatter plots

Rendered fromplots_scatter.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2020-10-12
Started: 2017-07-17

4.2 - Schematic plots

Rendered fromplots_schematic.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-10-20
Started: 2017-07-17

4.3 - Motif enrichment plots

Rendered fromplots_motif_enrichment.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2020-04-14
Started: 2017-07-17

4.4 - Regulatory TF plots

Rendered fromplots_TF.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-05-07
Started: 2017-07-17

4.5 - Heatmap plots

Rendered fromplots_heatmap.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2020-10-12
Started: 2017-10-25

5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUI

Rendered fromanalysis_gui.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2020-10-12
Started: 2017-07-17

Help page	Topics
Calculate the distance between probe and gene TSS	addDistNearestTSS
Adds mutation information to MAE	addMutCol
Calculate distance from region to nearest TSS	calcDistNearestTSS
Calculate motif Erichment	calculateEnrichement
Create a bigwig file for IGV visualization of DNA methylation data (Array)	createBigWigDNAmetArray
Create a junction track for IGV visualization of interection	createIGVtrack
Construct a Multi Assay Experiment for ELMER analysis	createMAE
Get family of transcription factors	createMotifRelevantTfs
Create summary document for TCGA.pipe function	createSummaryDocument
Create examples files for Sample mapping and information used in createMAE function	createTSVTemplates
ELMER (Enhancer Linking by Methylation/Expression Relationships)	ELMER
Use Hocomoco motif and homer to identify motifs in a given region	findMotifRegion
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 Pvalue	Get.Pvalue.p
summarize MR TF as a binary table with 1 if TF was found in the analysis, 0 if not	get.tab
Creating matrix for MR TF heatmap	get.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 MAE	getExp
Get Gene expression object samples from MAE	getExpSamples
getGeneID to report gene id from symbol	getGeneID
Get DNA methylation object from MAE	getMet
Get DNA methylation object samples from MAE	getMetSamples
GetNearGenes to collect nearby genes for one locus.	GetNearGenes
Get random pairs	getRandomPairs
Identifies nearest genes to a region	getRegionNearGenes
getRNAseq to download all RNAseq data for a certain cancer type from TCGA.	getRNAseq
getSymbol to report gene symbol from id	getSymbol
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 database	getTF
Get MR TF binding regions infered by ELMER	getTFBindingSites
Get TF target genes	getTFtargets
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-correlated	heatmapPairs
lable linear regression formula	lm_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 ORs	motif.enrichment.plot
Filtering probes	preAssociationProbeFiltering
promoterMeth to calculate associations of gene expression with DNA methylation at promoter regions	promoterMeth
Build report for TCGA.pipe function	render_report
scatter	scatter
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.meth	Stat.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.permu	Stat.nonpara.permu
Make MR TF binary table	summarizeTF
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 TF	TFsurvival.plot

Package: ELMER 2.31.0

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

ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

11 - ELMER: Use case

2 - Introduction: Input data

3.1 - Data input - Creating MAE object

3.2 - Identifying differentially methylated probes

3.3 - Identifying putative probe-gene pairs

3.4 - Motif enrichment analysis on the selected probes

3.5 - Identifying regulatory TFs

3.6 - TCGA.pipe: Running ELMER for TCGA data in a compact way

4.1 - Scatter plots

4.2 - Schematic plots

4.3 - Motif enrichment plots

4.4 - Regulatory TF plots

4.5 - Heatmap plots

5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUI

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)