Files in frankRuehle/systemsbio
Streamlined Analysis and Integration of Systems Biology Data

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/GEX_QC_expressionset.R R/GEX_process_dds.R R/GEX_process_eset.R R/GEX_readData2eset.R R/GEX_read_Illu_expr_array.R R/GEX_wrapDESeq2.R R/GEX_wrapLimma.R R/GT_genoAssoc.R R/GT_genoQC.R R/GT_readGeno.R R/HLP_LNCipedia.R R/HLP_attach_packages.R R/HLP_basic_SNP_annotation.R R/HLP_basic_gene_annotation.R R/HLP_filterGeneLists.R R/HLP_geneRanges.R R/HLP_genelabels_plot.R R/HLP_makeDomainsFromExons.R R/MT_QC_methylation.R R/MT_process_meth.R R/MT_read_Illu_meth450k.R R/MT_wrapMinfi.R R/SYB_plot_region.R R/SYB_wrapClusterProfiler.R R/SYB_wrapMatrixEQTL.R R/SYB_wrapPCAgoprom.R R/SYB_wrapPWMEnrich.R R/SYB_wrapRDAVID.R R/SYB_wrapWGCNA.R R/data.R R/pcaGOPromoter__pcaInfoPlot_org__bug_fixed.R README.md data-raw/prepare_example_data.R
data/gex.rda
inst/doc/figures/Heatmap_Module-Groupset_relationship.png
inst/doc/figures/Heatmap_example_case1-control.png
inst/doc/figures/Intramodular_analysis_case1-control.png
inst/doc/figures/ModuleDendrogram_Block.png
inst/doc/figures/Thumbs.db
inst/doc/figures/Venn_Diagram_example_allcomp.png
inst/doc/figures/Volcano_example_case1-control.png
inst/doc/figures/example_SampleDendrogram_noNorm_adjacency.png
inst/doc/figures/example_boxplot_controlprofile.png
inst/doc/figures/example_case1-control_Overrep_BP_cnetPlot.png
inst/doc/figures/example_case1-control_Overrep_BP_enrichmentMap.png
inst/doc/figures/example_case1-control_Overrep_BP_resulttable.txt
inst/doc/figures/example_case1-control_PWMEnrich_report.txt
inst/doc/figures/example_case1-control_PWMEnrich_top.png
inst/doc/figures/example_case2-control_PWMEnrich_top.png
inst/doc/figures/example_pcainfoplot_PC1_2.png
inst/doc/figures/example_pcaplot3d_PC1_2_3.png
inst/doc/figures/module_boxplot_1_of_3.png
inst/doc/figures/quality_metrics/arrayQualityMetrics.css
inst/doc/figures/quality_metrics/arrayQualityMetrics.js
inst/doc/figures/quality_metrics/box.pdf
inst/doc/figures/quality_metrics/box.png
inst/doc/figures/quality_metrics/dens.pdf
inst/doc/figures/quality_metrics/dens.svg
inst/doc/figures/quality_metrics/hm.pdf
inst/doc/figures/quality_metrics/hm.png
inst/doc/figures/quality_metrics/index.html
inst/doc/figures/quality_metrics/ma.pdf
inst/doc/figures/quality_metrics/ma.png
inst/doc/figures/quality_metrics/msd.pdf
inst/doc/figures/quality_metrics/msd.png
inst/doc/figures/quality_metrics/out box.pdf
inst/doc/figures/quality_metrics/out box.png
inst/doc/figures/quality_metrics/out hm.pdf
inst/doc/figures/quality_metrics/out hm.png
inst/doc/figures/quality_metrics/out ma.pdf
inst/doc/figures/quality_metrics/out ma.png
inst/doc/figures/quality_metrics/pca.pdf
inst/doc/figures/quality_metrics/pca.svg
inst/doc/systemsbio.R inst/doc/systemsbio.Rmd
inst/doc/systemsbio.html
man/QC_expressionset.Rd man/QC_methylation.Rd man/attach_package.Rd man/basicAnno.Rd man/basic_SNP_annotation.Rd man/determineNonOverlapGenelayers.Rd man/filterGeneLists.Rd man/genoAssoc.Rd man/genoQC.Rd man/gex.Rd man/makeDomainsFromExons.Rd man/plot.region.Rd man/processLNCipedia.Rd man/process_dds.Rd man/process_eset.Rd man/process_meth.Rd man/readData2eset.Rd man/readGeno.Rd man/read_Illu_expr_array.Rd man/read_Illu_meth450k.Rd man/regionalplot.genelabels.Rd man/subsetByOverlaps.keepAllMeta.Rd man/wrapClusterProfiler.Rd man/wrapDESeq2.Rd man/wrapLimma.Rd man/wrapMatrixEQTL.Rd man/wrapMinfi.Rd man/wrapPCAgoprom.Rd man/wrapPWMEnrich.Rd man/wrapRDAVID.Rd man/wrapWGCNA.Rd
systemsbio.Rproj
vignettes/systemsbio.Rmd
vignettes/systemsbio.html
frankRuehle/systemsbio documentation built on Oct. 25, 2018, 10:11 a.m.