Files in cnsb-boston/Omics_Notebook
What the package does (short line)
.dockerignore
.gitignore
Config.R
DESCRIPTION
Debug.R
Dockerfile
Dockerfile-base
NAMESPACE
Notebook.R
Notebook.py
NotebookGUI.R
R/checkColor.R
R/drawEnrichment.R
R/drawHeatmaps.R
R/drawPCA.R
R/drawRange.R
R/drawVenn.R
R/drawVolcano.R
R/drawXYCorr.R
R/g_S3.R
R/g_diff.R
R/g_enrichment.R
R/g_expl.R
R/g_integ.R
R/g_legend.R
R/getUniprotAnnotation.R
R/globals.R
R/intensityNorm.R
R/interactiveHeatmap.R
R/interactiveVolcano.R
R/makeEset.R
R/runEnrichR.R
R/runGSEA.R
R/saveFiles.R
R/variationPlot.R
R/writeDataToSheets.R
docs/README.md
inst/extdata/feature/MatchedFeatureSets.txt
inst/extdata/feature/MatchedFeatureSets_Full.txt
inst/extdata/feature/feature_eco_kegg.gmt.bz2
inst/extdata/feature/feature_expanded_eco_kegg.gmt.bz2
inst/extdata/feature/feature_expanded_fly_dme_biocyc.gmt.bz2
inst/extdata/feature/feature_expanded_human_hsa_biocyc.gmt.bz2
inst/extdata/feature/feature_expanded_human_hsa_mfn.gmt.bz2
inst/extdata/feature/feature_expanded_mouse_mmu_biocyc.gmt.bz2
inst/extdata/feature/feature_expanded_yeast_sce_biocyc.gmt.bz2
inst/extdata/feature/feature_fly_dme_biocyc.gmt.bz2
inst/extdata/feature/feature_human_hsa_biocyc.gmt.bz2
inst/extdata/feature/feature_human_hsa_mfn.gmt.bz2
inst/extdata/feature/feature_mouse_mmu_biocyc.gmt.bz2
inst/extdata/feature/feature_targetSize_eco_kegg.gmt.bz2
inst/extdata/feature/feature_targetSize_fly_dme_biocyc.gmt.bz2
inst/extdata/feature/feature_targetSize_human_hsa_biocyc.gmt.bz2
inst/extdata/feature/feature_targetSize_human_hsa_mfn.gmt.bz2
inst/extdata/feature/feature_targetSize_mouse_mmu_biocyc.gmt.bz2
inst/extdata/feature/feature_targetSize_yeast_sce_biocyc.gmt.bz2
inst/extdata/feature/feature_yeast_sce_biocyc.gmt.bz2
inst/extdata/geneset_table.txt
inst/extdata/matched/MatchedGeneSets.txt
inst/extdata/matched/gene_eco_kegg.gmt.bz2
inst/extdata/matched/gene_expanded_eco_kegg.gmt.bz2
inst/extdata/matched/gene_expanded_fly_dme_biocyc.gmt.bz2
inst/extdata/matched/gene_expanded_human_hsa_biocyc.gmt.bz2
inst/extdata/matched/gene_expanded_human_hsa_mfn.gmt.bz2
inst/extdata/matched/gene_expanded_mouse_mmu_biocyc.gmt.bz2
inst/extdata/matched/gene_expanded_yeast_sce_biocyc.gmt.bz2
inst/extdata/matched/gene_fly_dme_biocyc.gmt.bz2
inst/extdata/matched/gene_human_hsa_biocyc.gmt.bz2
inst/extdata/matched/gene_human_hsa_mfn.gmt.bz2
inst/extdata/matched/gene_mouse_mmu_biocyc.gmt.bz2
inst/extdata/matched/gene_targetSize_eco_kegg.gmt.bz2
inst/extdata/matched/gene_targetSize_fly_dme_biocyc.gmt.bz2
inst/extdata/matched/gene_targetSize_human_hsa_biocyc.gmt.bz2
inst/extdata/matched/gene_targetSize_human_hsa_mfn.gmt.bz2
inst/extdata/matched/gene_targetSize_mouse_mmu_biocyc.gmt.bz2
inst/extdata/matched/gene_targetSize_yeast_sce_biocyc.gmt.bz2
inst/extdata/matched/gene_yeast_sce_biocyc.gmt.bz2
inst/extdata/metaboAnalyst/cel_kegg.rds
inst/extdata/metaboAnalyst/dme_biocyc.rds
inst/extdata/metaboAnalyst/dme_kegg.rds
inst/extdata/metaboAnalyst/dre_kegg.rds
inst/extdata/metaboAnalyst/dre_mtf.rds
inst/extdata/metaboAnalyst/eco_kegg.rds
inst/extdata/metaboAnalyst/hsa_biocyc.rds
inst/extdata/metaboAnalyst/hsa_mfn.rds
inst/extdata/metaboAnalyst/mmu_biocyc.rds
inst/extdata/metaboAnalyst/mmu_kegg.rds
inst/extdata/metaboAnalyst/rno_kegg.rds
inst/extdata/metaboAnalyst/sce_biocyc.rds
inst/extdata/metaboAnalyst/sce_kegg.rds
inst/extdata/metabolite_model_table.txt
inst/extdata/species_genesets/Caenorhabditis_elegans_GSEA_GO_sets_all_symbols_April_2015.gmt.bz2
inst/extdata/species_genesets/Danio_rerio_GSEA_GO_sets_all_symbols_April_2015.gmt.bz2
inst/extdata/species_genesets/Drosophila_melanogaster_GSEA_GO_sets_all_symbols_April_2015.gmt.bz2
inst/extdata/species_genesets/Drosophila_melanogaster_fruit-fly_gmt2.gmt.bz2
inst/extdata/species_genesets/Escherichia_coli_str_K12_substr_MG1655_GSEA_GO_sets_all_symbols_April_2015.gmt.bz2
inst/extdata/species_genesets/Mus_musculus_GSEA_GO_sets_all_symbols_April_2015.gmt.bz2
inst/extdata/species_genesets/Rattus_norvegicus_GSEA_GO_sets_all_symbols_April_2015.gmt.bz2
inst/extdata/species_genesets/Saccharomyces_cerevisiae_S288c_GSEA_GO_sets_all_symbols_April_2015.gmt.bz2
inst/extdata/species_genesets/YeastDatabase_all_gmt.gmt.bz2
inst/extdata/species_genesets/escherichia_coli_k12_intestinalbacteria_gmt2.gmt.bz2
inst/extdata/species_genesets/rattus_norvegicus_brown-rat_gmt2.gmt.bz2
inst/extdata/species_genesets/xenopus_tropicalis_frog_gmt2.gmt.bz2
install.R
src/Notebook.Rmd
src/Notebook_1_Expl.Rmd
src/Notebook_2_Diff.Rmd
src/Notebook_3_Enrch.Rmd
src/Notebook_4_Integ.Rmd
src/Pipeline.R
src/Pipeline_Norm.R
