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/HLP_plot_volcano.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
doc/systemsbio.R
doc/systemsbio.Rmd
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/plot_volcano.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/figures/Heatmap_Module-Groupset_relationship.png
vignettes/figures/Heatmap_example_case1-control.png
vignettes/figures/Intramodular_analysis_case1-control.png
vignettes/figures/ModuleDendrogram_Block.png
vignettes/figures/Thumbs.db
vignettes/figures/Venn_Diagram_example_allcomp.png
vignettes/figures/Volcano_example_case1-control.png
vignettes/figures/example_SampleDendrogram_noNorm_adjacency.png
vignettes/figures/example_boxplot_controlprofile.png
vignettes/figures/example_case1-control_Overrep_BP_cnetPlot.png
vignettes/figures/example_case1-control_Overrep_BP_enrichmentMap.png
vignettes/figures/example_case1-control_Overrep_BP_resulttable.txt
vignettes/figures/example_case1-control_PWMEnrich_report.txt
vignettes/figures/example_case1-control_PWMEnrich_top.png
vignettes/figures/example_case2-control_PWMEnrich_top.png
vignettes/figures/example_pcainfoplot_PC1_2.png
vignettes/figures/example_pcaplot3d_PC1_2_3.png
vignettes/figures/module_boxplot_1_of_3.png
vignettes/quality_metrics/arrayQualityMetrics.css
vignettes/quality_metrics/arrayQualityMetrics.js
vignettes/quality_metrics/box.pdf
vignettes/quality_metrics/box.png
vignettes/quality_metrics/dens.pdf
vignettes/quality_metrics/dens.svg
vignettes/quality_metrics/hm.pdf
vignettes/quality_metrics/hm.png
vignettes/quality_metrics/index.html
vignettes/quality_metrics/ma.pdf
vignettes/quality_metrics/ma.png
vignettes/quality_metrics/msd.pdf
vignettes/quality_metrics/msd.png
vignettes/quality_metrics/out_box.pdf
vignettes/quality_metrics/out_box.png
vignettes/quality_metrics/out_hm.pdf
vignettes/quality_metrics/out_hm.png
vignettes/quality_metrics/out_ma.pdf
vignettes/quality_metrics/out_ma.png
vignettes/quality_metrics/pca.pdf
vignettes/quality_metrics/pca.svg
vignettes/systemsbio.Rmd
