Files in hms-dbmi/drugseqr
Finds CMAP02/L1000 Compounds That Oppose Gene Expression Signatures.

.Rbuildignore
.Rprofile
.dockerignore
.gitignore
.renvignore
DESCRIPTION
Dockerfile
NAMESPACE
R/DimPlot.R R/FeaturePlot.R R/add_es.R R/diff_utils.R R/dropdownButton.R R/format_query_table.R R/get_drugs_table.R R/heatplot.R R/load_scseq.R R/load_seq.R R/modules-bulk-server.R R/modules-bulk-ui.R R/modules-bulk-utils.R R/modules-docs-ui.R R/modules-drugs-server.R R/modules-drugs-ui.R R/modules-drugs-utils.R R/modules-path-utils.R R/modules-sc-server.R R/modules-sc-ui.R R/modules-sc-utils.R R/parse_pug.R R/pbulk_qcsets.R R/plot_scseq.R R/query_utils.R R/remove_sva.R R/run_drugseqr.R R/run_kallisto_bulk.R R/run_kallisto_scseq.R R/run_salmon_bulk.R R/scseq_qc.R R/scseq_reports.R R/select_contrast.R R/select_pairs.R R/server-utils.R
R/sysdata.rda
R/ui-utils.R README.md data-raw/benchmarks/rnaseq_microarray_cmap/1-diff_expr.R data-raw/benchmarks/rnaseq_microarray_cmap/2-salmon_vs_kallisto.R data-raw/benchmarks/rnaseq_microarray_cmap/3-rnaseq_vs_microarray.R
data-raw/cell_info/GSE92742_Broad_LINCS_cell_info.txt
data-raw/cell_info/cell_info.R
data-raw/cell_info/cell_info.rds
data-raw/d3/box.js
data-raw/d3/morley.css
data-raw/d3/morley.csv
data-raw/d3/morley.js
data-raw/d3/simplot.js
data-raw/drug_annot/pug_view/check_sider.R
data-raw/drug_annot/pug_view/cids.csv
data-raw/drug_annot/pug_view/cids.rds
data-raw/drug_annot/pug_view/get_cids.R
data-raw/drug_annot/pug_view/get_views.sh
data-raw/drug_annot/pug_view/pug_annot.R
data-raw/drug_annot/pug_view/pug_annot.rds
data-raw/drug_annot/pug_view/sider.rds
data-raw/drug_annot/repurposing_drugs_20180907.txt
data-raw/drug_annot/repurposing_samples_20180907.txt
data-raw/drug_annot/setup.R data-raw/drug_es/pvals.R data-raw/drug_es/setup.R data-raw/drug_es/signatures.R data-raw/drug_gene_queries/drug_gene_queries.R data-raw/drug_gene_queries/pert_names.R
data-raw/drug_gene_queries/pert_names.rds
data-raw/drug_paths/cmap_paths.R data-raw/drug_paths/l1000_paths.R
data-raw/drug_paths/map.rds
data-raw/example_data/GSE134809_samples.csv
data-raw/example_data/GSE93624_annot.csv
data-raw/example_data/setup.R data-raw/genes/genes.R
data-raw/genes/genes.rds
data-raw/homologene/homologene.R
data-raw/homologene/homologene.rds
data-raw/homologene/hs.rds
data-raw/padog/gs.names.go.rds
data-raw/padog/gs.names.rds
data-raw/padog/gslist.go.rds
data-raw/padog/gslist.rds
data-raw/padog/padog.R
data-raw/single-cell/alevin-args/1-txp2gene.sh
data-raw/single-cell/alevin-args/2-txp2hgnc.R data-raw/single-cell/alevin-args/3-mrna_rrna.R
data-raw/single-cell/alevin-args/ribo.txt
data-raw/single-cell/alevin-args/ribo_mouse.csv
data-raw/single-cell/alevin-args/txp2gene.tsv
data-raw/single-cell/batch_convert.R data-raw/single-cell/batch_quant.R data-raw/single-cell/benchmark/gse_names.R data-raw/single-cell/biogps/biogps.R
data-raw/single-cell/biogps/biogps.rds
data-raw/single-cell/dtangle.genes.R data-raw/sysdata.R data-raw/tx2gene/tx2gene.R
data-raw/tx2gene/tx2gene.rds
data-raw/tx2gene/tx2gene_mouse.rds
drugseqr.Rproj
inst/app/global.R inst/app/server.R inst/app/tests/data/setup-static.R inst/app/tests/shinytest.R inst/app/ui.R
inst/app/www/EMBL_Logo.png
inst/app/www/anchor-polyfill.js
inst/app/www/bs-docs.css
inst/app/www/bulk_intro.csv
inst/app/www/contextMenu.js
inst/app/www/custom.css
inst/app/www/drugbank_logo.ico
inst/app/www/drugs.css
inst/app/www/drugs_intro.csv
inst/app/www/genecards_logo.ico
inst/app/www/pathways.css
inst/app/www/pubchem_logo.ico
inst/app/www/renderSelectize.js
inst/app/www/sc_intro.csv
inst/app/www/toggleClinicalTitle.js
inst/app/www/wiki_logo.svg
inst/extdata/CMAP02_annot.rds
inst/extdata/CMAP02_pdata.rds
inst/extdata/IBD/IBD_1000 - 1285-01-G10_S20_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G1_S9_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G2_S10_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G3_S11_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G4_S12_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G5_S13_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G6-1_S14_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G6-2_S15_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G7-1_S16_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G7-2_S17_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G8_S18_R1_001.fastq.gz
inst/extdata/IBD/IBD_1000 - 1285-01-G9_S19_R1_001.fastq.gz
inst/extdata/IBD/Phenotypes.csv
inst/extdata/IBD/dgel.rds
inst/extdata/IBD/eset.rds
inst/extdata/IBD/pdata.rds
inst/extdata/L1000_annot.rds
inst/extdata/L1000_drugs_annot.rds
inst/extdata/L1000_drugs_pdata.rds
inst/extdata/L1000_genes_annot.rds
inst/extdata/L1000_genes_pdata.rds
inst/extdata/L1000_pdata.rds
inst/extdata/mrna.csv
inst/extdata/mrna_mouse.csv
inst/extdata/rrna.csv
inst/extdata/rrna_mouse.csv
inst/extdata/txp2hgnc.tsv
man/AutoPointSize.Rd man/CombinePlots.Rd man/DimPlot.Rd man/FeaturePlot.Rd man/GetXYAesthetics.Rd man/LabelClusters.Rd man/NoLegend.Rd man/Read10X.Rd man/Read10X_h5.Rd man/SingleDimPlot.Rd man/add_adjusted.Rd man/add_combined_metrics.Rd man/add_doublet_score.Rd man/add_es.Rd man/add_hvgs.Rd man/add_integrated_ambient.Rd man/add_linkout.Rd man/add_scseq_clusters.Rd man/add_scseq_qc_metrics.Rd man/add_scseq_qcplot_metrics.Rd man/add_table_html.Rd man/add_vsd.Rd man/advancedOptions.Rd man/advancedOptionsInput.Rd man/annot_query_res.Rd man/append_annot.Rd man/boxPlotly.Rd man/build_ensdb.Rd man/bulkAnal.Rd man/bulkAnalInput.Rd man/bulkAnnot.Rd man/bulkAnnotInput.Rd man/bulkCellsPlotly.Rd man/bulkDataset.Rd man/bulkDatasetInput.Rd man/bulkEndType.Rd man/bulkExploreTable.Rd man/bulkForm.Rd man/bulkFormAnal.Rd man/bulkFormAnalInput.Rd man/bulkFormInput.Rd man/bulkFormQuant.Rd man/bulkFormQuantInput.Rd man/bulkGenePlotly.Rd man/bulkMDS.Rd man/bulkMDSplotly.Rd man/bulkPage.Rd man/bulkPageUI.Rd man/bulkPlotlyUI.Rd man/bulkQuantTable.Rd man/bulkTable.Rd man/calcx.Rd man/check_bulk_changed.Rd man/check_gras.Rd man/check_is_cellranger.Rd man/clean_y.Rd man/clusterComparison.Rd man/clusterComparisonInput.Rd man/collapse_sorted.Rd man/comparisonType.Rd man/comparisonTypeToggle.Rd man/construct_eset.Rd man/construct_path_df.Rd man/construct_pbulk_esets.Rd man/construct_pbulk_qcsets.Rd man/create_scseq.Rd man/customQueryForm.Rd man/customQueryFormInput.Rd man/decide_ambient.Rd man/detect_10x_chemistry.Rd man/detect_cells.Rd man/detect_paired.Rd man/diff_abundance.Rd man/disableAll.Rd man/dist.Rd man/dl_10x_whitelists.Rd man/dl_pert_pvals.Rd man/dl_pert_result.Rd man/dl_pert_signature.Rd man/docsPageUI.Rd man/docsSection.Rd man/docsSideNav.Rd man/docsSubsection.Rd man/dropdownButton.Rd man/dropdownMenuButton.Rd man/drugsFormInput.Rd man/drugsGenesPlotly.Rd man/drugsGenesPlotlyOutput.Rd man/drugsPage.Rd man/drugsPageUI.Rd man/drugsTable.Rd man/drugsTableOutput.Rd man/dtangleForm.Rd man/dtangleFormInput.Rd man/enableAll.Rd man/evaluate_custom_metric.Rd man/exist_clusters.Rd man/exploreEset.Rd man/extract_section_info.Rd man/filter_clinical.Rd man/filter_genes.Rd man/filter_nsig.Rd man/fit_ebayes.Rd man/fit_lm.Rd man/fit_lm_scseq.Rd man/format_dl_annot.Rd man/format_query_res.Rd man/format_up_annot.Rd man/format_up_custom.Rd man/from_crossmeta.Rd man/get_10x_whitepath.Rd man/get_boxplotly_cell_args.Rd man/get_boxplotly_gene_args.Rd man/get_cell_choices.Rd man/get_cluster_choices.Rd man/get_cluster_markers.Rd man/get_cluster_stats.Rd man/get_contrast_choices.Rd man/get_contrast_markers.Rd man/get_cors_html.Rd man/get_dprimes.Rd man/get_drug_paths.Rd man/get_drugbank.Rd man/get_drugs_table.Rd man/get_ensdb_package.Rd man/get_exclude_choices.Rd man/get_fastq_id1s.Rd man/get_founder.Rd man/get_gene_choices.Rd man/get_group_levels.Rd man/get_gs.names.Rd man/get_gslist.Rd man/get_integrated_ambient.Rd man/get_kallisto_index.Rd man/get_kegg_species.Rd man/get_label_plot.Rd man/get_label_transfer_choices.Rd man/get_mds.Rd man/get_metric_choices.Rd man/get_metric_features.Rd man/get_mods.Rd man/get_nearest_row.Rd man/get_npc_choices.Rd man/get_open_a.Rd man/get_outliers.Rd man/get_palette.Rd man/get_path_df.Rd man/get_path_directions.Rd man/get_path_res.Rd man/get_pct_ambient.Rd man/get_pkg_version.Rd man/get_pred_annot.Rd man/get_query_cols.Rd man/get_sc_dataset_choices.Rd man/get_scseq_markers.Rd man/get_species.Rd man/get_top.Rd man/get_top_cors.Rd man/get_top_table.Rd man/get_tsne_coords.Rd man/get_tx2gene.Rd man/get_wikipedia.Rd man/heatplot.Rd man/html_space.Rd man/id_from_tab.Rd man/identify_sc_files.Rd man/import_quants.Rd man/init_drugseqr.Rd man/integrate_saved_scseqs.Rd man/integrate_scseqs.Rd man/integrationForm.Rd man/integrationFormInput.Rd man/interpret.Rd man/iqr_replicates.Rd man/isTruthyAll.Rd man/is_invertible.Rd man/justifiedButtonGroup.Rd man/labelTransferForm.Rd man/labelTransferFormInput.Rd man/limit_cells.Rd man/load_bulk_anals.Rd man/load_bulk_datasets.Rd man/load_cellranger_counts.Rd man/load_custom_anals.Rd man/load_custom_results.Rd man/load_drug_es.Rd man/load_kallisto_counts.Rd man/load_pert_anals.Rd man/load_pert_signature.Rd man/load_raw_scseq.Rd man/load_scseq.Rd man/load_scseq_datasets.Rd man/load_scseq_qcgenes.Rd man/load_scseq_subsets.Rd man/load_seq.Rd man/merge_linkouts.Rd man/navbarUI.Rd man/normalize_scseq.Rd man/pairwise_wilcox.Rd man/plot_biogps.Rd man/plot_cluster_labels.Rd man/plot_dprimes.Rd man/plot_ridge.Rd man/plot_scseq_dprimes.Rd man/plot_tsne_cluster.Rd man/plot_tsne_feature.Rd man/plot_tsne_feature_sample.Rd man/plotlyMDS.Rd man/process_raw_scseq.Rd man/query_budger.Rd man/query_drugs.Rd man/readRDS.safe.Rd man/remove_bulk_anals.Rd man/remove_dataset_files.Rd man/remove_sva.Rd man/rightClickMenu.Rd man/run_custom_query.Rd man/run_dream.Rd man/run_drug_queries.Rd man/run_drugseqr.Rd man/run_fastmnn.Rd man/run_harmony.Rd man/run_kallisto_bulk.Rd man/run_kallisto_scseq.Rd man/run_kallisto_scseq_commands.Rd man/run_liger.Rd man/run_limma.Rd man/run_limma_scseq.Rd man/run_lmfit.Rd man/run_salmon_bulk.Rd man/run_scseq_qc.Rd man/run_sva.Rd man/run_tsne.Rd man/run_varPart.Rd man/save_bulk_anals.Rd man/save_lmfit.Rd man/save_scle.Rd man/save_scseq_args.Rd man/save_scseq_data.Rd man/scBioGpsPlot.Rd man/scBioGpsPlotOutput.Rd man/scClusterPlot.Rd man/scClusterPlotOutput.Rd man/scForm.Rd man/scFormInput.Rd man/scLabelsComparison.Rd man/scLabelsPlot.Rd man/scLabelsPlotOutput.Rd man/scMarkerPlot.Rd man/scMarkerPlotOutput.Rd man/scPage.Rd man/scPageUI.Rd man/scRidgePlot.Rd man/scRidgePlotOutput.Rd man/scSampleComparison.Rd man/scSampleComparisonInput.Rd man/scSampleMarkerPlot.Rd man/scSampleMarkerPlotOutput.Rd man/scSelectedDataset.Rd man/scSelectedDatasetInput.Rd man/sc_dl_filename.Rd man/scseq_part_path.Rd man/select_contrast.Rd man/select_pairs.Rd man/selectedAnal.Rd man/selectedAnalInput.Rd man/selectedAnnotDatasetInput.Rd man/selectedDrugStudy.Rd man/selectedDrugStudyInput.Rd man/selectedGene.Rd man/selectedGeneInput.Rd man/selectedPertSignature.Rd man/selectedPertSignatureInput.Rd man/setup_fdata.Rd man/shorten_cluster_labels.Rd man/sort_query_table_clin.Rd man/standardize_cellranger.Rd man/subsetForm.Rd man/subsetFormInput.Rd man/subset_saved_scseq.Rd man/summarise_query_table.Rd man/summarize_compound.Rd man/supress.genes.Rd man/svaButton.Rd man/tabPane.Rd man/theme_dimgray.Rd man/theme_no_xaxis.Rd man/theme_no_yaxis.Rd man/validate_custom_query.Rd man/validate_integration.Rd man/validate_metric.Rd man/validate_pairs.Rd man/validate_pdata.Rd man/validate_preds.Rd man/validate_reps.Rd man/validate_up_annot.Rd man/validate_up_custom.Rd
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
tests/testthat.R tests/testthat/test-app.R tests/testthat/test_calcx.R tests/testthat/test_diff_expr.R tests/testthat/test_diff_setup.R tests/testthat/test_linkouts.R tests/testthat/test_load.R tests/testthat/test_paired.R tests/testthat/test_pairs.R tests/testthat/test_pdata.R tests/testthat/test_reps.R tests/testthat/test_salmon.R tests/testthat/test_summarize_compound.R
hms-dbmi/drugseqr documentation built on Aug. 8, 2020, 2:03 a.m.