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

NAMESPACE
DESCRIPTION
R/TFsurvival.plot.R R/Scatter.plot.R R/GetNearbyGenes.R R/FetchTCGA.R R/TCGA_pipe.R R/ELMER.R R/boxPlot.R R/Schematic.plot.R R/motif.TF.Plots.R R/methodAccess.R R/Main_function.R R/Small.R R/StatisticTest.R man/GetNearGenes.Rd man/TF.rank.plot.Rd man/Get.Pvalue.p.Rd man/preAssociationProbeFiltering.Rd man/lm_eqn.Rd man/scatter.plot.Rd man/get.permu.Rd man/getExpSamples.Rd man/ELMER.Rd man/getExp.Rd man/metBoxPlot.Rd man/motif.enrichment.plot.Rd man/getMet.Rd man/createMAE.Rd man/createTSVTemplates.Rd man/Stat.diff.meth.Rd man/get.enriched.motif.Rd man/Stat.nonpara.Rd man/get.diff.meth.Rd man/get.TFs.Rd man/getGeneID.Rd man/schematic.plot.Rd man/get.pair.Rd man/createMotifRelevantTfs.Rd man/addMutCol.Rd man/TCGA.pipe.Rd man/getClinic.Rd man/promoterMeth.Rd man/TFsurvival.plot.Rd man/getTF.Rd man/getMetSamples.Rd man/getRNAseq.Rd man/get450K.Rd man/createSummaryDocument.Rd man/getSymbol.Rd man/heatmapPairs.Rd man/getTSS.Rd man/Stat.nonpara.permu.Rd man/scatter.Rd man/get.feature.probe.Rd man/getTCGA.Rd man/addDistNearestTSS.Rd inst/doc/plots_schematic.R
inst/doc/analysis_data_input.html
inst/doc/plots_motif_enrichment.R
inst/doc/analysis_gui.html
inst/doc/plots_heatmap.Rmd inst/doc/input.R inst/doc/plots_scatter.Rmd
inst/doc/input.html
inst/doc/plots_scatter.html
inst/doc/plots_schematic.Rmd
inst/doc/pipe.html
inst/doc/analysis_regulatory_tf.html
inst/doc/analysis_data_input.R inst/doc/analysis_regulatory_tf.Rmd inst/doc/input.Rmd inst/doc/analysis_diff_meth.R
inst/doc/plots_heatmap.html
inst/doc/analysis_gui.Rmd
inst/doc/plots_TF.html
inst/doc/analysis_get_pair.html
inst/doc/index.html
inst/doc/analysis_regulatory_tf.R inst/doc/analysis_get_pair.Rmd
inst/doc/analysis_diff_meth.html
inst/doc/analysis_gui.R
inst/doc/plots_motif_enrichment.html
inst/doc/plots_TF.Rmd
inst/doc/plots_schematic.html
inst/doc/plots_TF.R inst/doc/index.Rmd inst/doc/pipe.R inst/doc/pipe.Rmd inst/doc/plots_scatter.R inst/doc/analysis_get_pair.R inst/doc/analysis_data_input.Rmd inst/doc/index.R inst/doc/plots_heatmap.R inst/doc/plots_motif_enrichment.Rmd inst/doc/analysis_diff_meth.Rmd
inst/doc/analysis_motif_enrichment.html
inst/doc/analysis_motif_enrichment.Rmd inst/doc/analysis_motif_enrichment.R vignettes/analysis_motif_enrichment.Rmd vignettes/plots_scatter.Rmd
vignettes/style.css
vignettes/plots_heatmap.Rmd
vignettes/bibliography.bib
vignettes/analysis_diff_meth.Rmd vignettes/analysis_gui.Rmd vignettes/plots_schematic.Rmd vignettes/input.Rmd vignettes/analysis_get_pair.Rmd vignettes/plots_motif_enrichment.Rmd
vignettes/workflow.png
vignettes/analysis_data_input.Rmd
vignettes/_site.yml
vignettes/pipe.Rmd vignettes/index.Rmd vignettes/plots_TF.Rmd vignettes/analysis_regulatory_tf.Rmd
vignettes/figures/elmer_data_saved.png
vignettes/figures/elmer_data_dnamet.png
vignettes/figures/elmer_visualize_plot_scatter_byProbe.png
vignettes/figures/elmer_visualize_table_pair.png
vignettes/figures/gui_dnamet_prepare.png
vignettes/figures/elmer_data_menu.png
vignettes/figures/elmer_analysis_data.png
vignettes/figures/workflow_TGCAbiolinks.png
vignettes/figures/elmer_visualize_table_sigprobes.png
vignettes/figures/elmer_visualize_plot_scatter_byTF.png
vignettes/figures/elmer_analysis_menu.png
vignettes/figures/elmer_visualize_table_tf.png
vignettes/figures/gui_se_sampleinfo.png
vignettes/figures/gui_visualize_se.png
vignettes/figures/gui_dnamet_prepare_completed.png
vignettes/figures/elmer_visualize_table_enriched_motif.png
vignettes/figures/elemer_visualize_motif_enrichment.png
vignettes/figures/elmer_analysis_TF.png
vignettes/figures/gui_exp_prepare_completed.png
vignettes/figures/elemer_visualize_schematic_gene.png
vignettes/figures/elmer_analysis_groups.png
vignettes/figures/gui_exp_se_assay.png
vignettes/figures/elmer_visualize_select1.png
vignettes/figures/elmer_data_dnamet_select.png
vignettes/figures/workflow.png
vignettes/figures/elmer_analysis_diffmeth.png
vignettes/figures/gui_exp_query_results.png
vignettes/figures/gui_se_selection.png
vignettes/figures/gui_exp_prepare.png
vignettes/figures/elmer_visualize_plot_scatter_byPair.png
vignettes/figures/elmer_visualize_select2.png
vignettes/figures/elmer_data_final.png
vignettes/figures/paper_get_pairs.png
vignettes/figures/gui_dnamet_plots.png
vignettes/figures/gui_exp_results.png
vignettes/figures/elmer_analysis_motif.png
vignettes/figures/elmer_data_exp_select.png
vignettes/figures/gui_exp_plots.png
vignettes/figures/elmer_visualize_results.png
vignettes/figures/elmer_analysis_pair.png
vignettes/figures/workflow_ELMER.png
vignettes/figures/elmer_visualize_tfraningplot.png
vignettes/figures/paper_get.pairs.png
vignettes/figures/gui_dnamet_query.png
vignettes/figures/elmer_analysis_message.png
vignettes/figures/gui_exp_se_features.png
vignettes/figures/gui_exp_query.png
vignettes/figures/gui_menu.png
vignettes/figures/paper_diff_meth.png
vignettes/figures/gui_se_select.png
vignettes/figures/elmer_data_exp.png
vignettes/figures/elemer_visualize_schematic_probe.png
vignettes/figures/folder_structure.png
vignettes/figures/elmer_analysis_final.png
build/vignette.rds
tests/testthat.R tests/testthat/test-get.enriched.motifs.R tests/testthat/test-data.R tests/testthat/test-createMAE.R tests/testthat/test-neargenes.R tests/testthat/test-get.pair.R tests/testthat/test-getTF.R tests/testthat/test-diffmet.R
ELMER documentation built on Dec. 9, 2017, 2:01 a.m.