Files in ELMER

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

NEWS.md

NAMESPACE

DESCRIPTION

build/vignette.rds

R/TFsurvival.plot.R R/Schematic.plot.R R/methodAccess.R R/TCGA_pipe.R R/FetchTCGA.R R/StatisticTest.R R/plots.R R/Small.R R/motif.TF.Plots.R R/ELMER.R R/Main_function.R R/Scatter.plot.R R/GetNearbyGenes.R vignettes/plots_motif_enrichment.Rmd vignettes/analysis_gui.Rmd

vignettes/bibliography.bib

vignettes/plots_heatmap.Rmd vignettes/index.Rmd vignettes/analysis_regulatory_tf.Rmd vignettes/usecase.Rmd vignettes/pipe.Rmd vignettes/input.Rmd

vignettes/_site.yml

vignettes/plots_scatter.Rmd

vignettes/hexELMER.png

vignettes/analysis_get_pair.Rmd vignettes/plots_schematic.Rmd vignettes/analysis_diff_meth.Rmd vignettes/analysis_motif_enrichment.Rmd vignettes/analysis_data_input.Rmd vignettes/plots_TF.Rmd

vignettes/style.css

vignettes/figures/elmer_data_exp_select.png

vignettes/figures/elmer_visualize_table_tf.jpg

vignettes/figures/gui_exp_prepare_completed.png

vignettes/figures/elmer_analysis_diffmeth.png

vignettes/figures/gui_exp_prepare.png

vignettes/figures/gui_dnamet_prepare_completed.png

vignettes/figures/elmer_data_final.jpg

vignettes/figures/workflow.png

vignettes/figures/elmer_data_dnamet.png

vignettes/figures/paper_get_pairs.jpg

vignettes/figures/gui_menu.png

vignettes/figures/elemer_visualize_schematic_gene.jpg

vignettes/figures/elmer_visualize_results.png

vignettes/figures/elmer_analysis_pair.png

vignettes/figures/elmer_visualize_plot_scatter_byTF.jpg

vignettes/figures/paper_get.pairs.jpg

vignettes/figures/elmer_analysis_groups.png

vignettes/figures/elmer_data_menu.png

vignettes/figures/gui_exp_query_results.jpg

vignettes/figures/gui_dnamet_prepare.png

vignettes/figures/elmer_visualize_table_sigprobes.jpg

vignettes/figures/elmer_data_dnamet_select.png

vignettes/figures/elemer_visualize_schematic_probe.jpg

vignettes/figures/paper_diff_meth.jpg

vignettes/figures/elmer_analysis_TF.png

vignettes/figures/elmer_visualize_select2.png

vignettes/figures/gui_visualize_se.png

vignettes/figures/elmer_visualize_tfraningplot.jpg

vignettes/figures/elmer_analysis_data.png

vignettes/figures/elemer_visualize_motif_enrichment.jpg

vignettes/figures/elmer_visualize_table_enriched_motif.jpg

vignettes/figures/gui_se_select.png

vignettes/figures/gui_exp_results.png

vignettes/figures/elmer_analysis_menu.png

vignettes/figures/elmer_analysis_final.png

vignettes/figures/elmer_analysis_motif.png

vignettes/figures/elmer_data_saved.png

vignettes/figures/elmer_data_exp.png

vignettes/figures/elmer_visualize_select1.png

vignettes/figures/elmer_analysis_message.png

man/getTF.Rd man/scatter.plot.Rd man/get.enriched.motif.Rd man/ELMER.Rd man/calcDistNearestTSS.Rd man/motif.enrichment.plot.Rd man/get.TFs.Rd man/createSummaryDocument.Rd man/getRandomPairs.Rd man/getClinic.Rd man/addMutCol.Rd man/get.tab.Rd man/getSymbol.Rd man/getTFBindingSites.Rd man/get.feature.probe.Rd man/get450K.Rd man/Stat.diff.meth.Rd man/getTFtargets.Rd man/Stat.nonpara.Rd man/getTCGA.Rd man/lm_eqn.Rd man/getRegionNearGenes.Rd man/render_report.Rd man/findMotifRegion.Rd man/TF.rank.plot.Rd man/createBigWigDNAmetArray.Rd man/getTSS.Rd man/createMotifRelevantTfs.Rd man/getMetSamples.Rd man/createMAE.Rd man/getExp.Rd man/get.permu.Rd man/get.pair.Rd man/getMet.Rd man/getExpSamples.Rd man/preAssociationProbeFiltering.Rd man/createIGVtrack.Rd man/scatter.Rd man/getGeneID.Rd man/heatmapPairs.Rd man/metBoxPlot.Rd man/get.tabs.Rd man/TCGA.pipe.Rd man/summarizeTF.Rd man/getRNAseq.Rd man/TFsurvival.plot.Rd man/calculateEnrichement.Rd man/addDistNearestTSS.Rd man/Get.Pvalue.p.Rd man/promoterMeth.Rd man/schematic.plot.Rd man/createTSVTemplates.Rd man/get.diff.meth.Rd man/heatmapGene.Rd man/GetNearGenes.Rd man/Stat.nonpara.permu.Rd tests/testthat.R tests/testthat/test-getTF.R tests/testthat/test-createMAE.R tests/testthat/test-neargenes.R tests/testthat/test-diffmet.R tests/testthat/test-getRandomPair.R tests/testthat/test-data.R tests/testthat/test-pipe.R tests/testthat/test-get.pair.R tests/testthat/test-get.enriched.motifs.R

inst/CITATION

inst/doc/plots_motif_enrichment.Rmd

inst/doc/plots_motif_enrichment.html

inst/doc/index.html

inst/doc/analysis_gui.Rmd

inst/doc/analysis_regulatory_tf.html

inst/doc/plots_heatmap.R

inst/doc/plots_heatmap.html

inst/doc/plots_TF.html

inst/doc/plots_TF.R inst/doc/plots_heatmap.Rmd

inst/doc/pipe.html

inst/doc/analysis_motif_enrichment.R inst/doc/index.Rmd inst/doc/usecase.R

inst/doc/plots_scatter.html

inst/doc/analysis_regulatory_tf.Rmd inst/doc/usecase.Rmd inst/doc/pipe.Rmd inst/doc/analysis_get_pair.R

inst/doc/analysis_data_input.html

inst/doc/input.Rmd inst/doc/analysis_gui.R

inst/doc/analysis_motif_enrichment.html

inst/doc/plots_schematic.html

inst/doc/input.R inst/doc/plots_scatter.Rmd inst/doc/analysis_get_pair.Rmd inst/doc/plots_scatter.R inst/doc/plots_schematic.Rmd

inst/doc/analysis_get_pair.html

inst/doc/plots_schematic.R

inst/doc/analysis_diff_meth.html

inst/doc/analysis_diff_meth.Rmd inst/doc/analysis_motif_enrichment.Rmd

inst/doc/input.html

inst/doc/analysis_diff_meth.R inst/doc/analysis_data_input.R

inst/doc/analysis_gui.html

inst/doc/analysis_data_input.Rmd inst/doc/plots_TF.Rmd inst/doc/plots_motif_enrichment.R inst/doc/index.R inst/doc/analysis_regulatory_tf.R

inst/doc/usecase.html

inst/doc/pipe.R inst/rmd/template.Rmd

inst/rmd/tabset-dropdown.html

inst/rmd/style.css

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.