Files in hms-dbmi/drugseqr
GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

.Rbuildignore
.Rprofile
.dockerignore
.gitignore
.renvignore
DESCRIPTION
Dockerfile
LICENSE
LICENSE.md
NAMESPACE
NEWS.md R/DimPlot.R R/FeaturePlot.R R/NNTransform.R R/SingleExIPlot.R R/diff_utils.R R/dropdownButton.R R/format_query_table.R R/from_crossmeta.R R/get_drugs_table.R R/load_scseq.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/run_dseqr.R R/run_esmeta.R R/run_kallisto_scseq.R R/scseq_qc.R R/scseq_reports.R R/server-utils.R
R/sysdata.rda
R/theme_pubr.R 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/biogps/biogps.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/convert/0.10.0.R data-raw/convert/0.13.0.R data-raw/convert/0.13.3.R data-raw/convert/0.14.0.R data-raw/convert/0.14.1.R data-raw/convert/0.15.0.R data-raw/convert/0.9.2.R
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/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_paths/cmap_paths.R data-raw/drug_paths/l1000_paths.R
data-raw/drug_paths/map.rds
data-raw/ensmap/ensmap.R
data-raw/ensmap/ensmap.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/macspectrum/amdsg_hgnc.txt
data-raw/macspectrum/amdsgs.rds
data-raw/macspectrum/macspectrum.R
data-raw/macspectrum/psg_amdsg_hgnc.txt
data-raw/macspectrum/psg_hgnc.txt
data-raw/macspectrum/psgs.rds
data-raw/qcgenes/mrna_rrna.R data-raw/sysdata.R
dseqr.Rproj
inst/app/global.R inst/app/server.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/favicon.png
inst/app/www/genecards_logo.ico
inst/app/www/isMobile.js
inst/app/www/pathways.css
inst/app/www/progressBinding.js
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/mrna.csv
inst/extdata/mrna_mouse.csv
inst/extdata/rrna.csv
inst/extdata/rrna_mouse.csv
inst/extdata/txp2hgnc.zip
man/AutoPointSize.Rd man/CheckDots.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/SingleExIPlot.Rd man/add_combined_metrics.Rd man/add_doublet_score.Rd man/add_hvgs.Rd man/add_integrated_ambient.Rd man/add_linkout.Rd man/add_scseq_qc_metrics.Rd man/add_scseq_qcplot_metrics.Rd man/add_table_html.Rd man/advancedOptionsInput.Rd man/annot_query_res.Rd man/append_annot.Rd man/boxPlotly.Rd man/boxPlotlyCells.Rd man/bulkPage.Rd man/bulkPageUI.Rd man/calcx.Rd man/check_bulk_changed.Rd man/check_gras.Rd man/check_is_cellranger.Rd man/collapse_sorted.Rd man/construct_path_df.Rd man/construct_pbulk_qcsets.Rd man/construct_pbulk_subsets.Rd man/create_scseq.Rd man/customQueryFormInput.Rd man/datasets_to_list.Rd man/detect_10x_chemistry.Rd man/detect_cells.Rd man/diff_abundance.Rd man/disableAll.Rd man/dl_10x_whitelists.Rd man/dl_pert_result.Rd man/dl_pert_signature.Rd man/docsPageUI.Rd man/downsample_clusters.Rd man/downsample_group.Rd man/dropdownButtonMod.Rd man/dropdownMenuButton.Rd man/drugsFormInput.Rd man/drugsGenesPlotlyOutput.Rd man/drugsPage.Rd man/drugsPageUI.Rd man/drugsTableOutput.Rd man/enableAll.Rd man/evaluate_custom_metric.Rd man/exist_clusters.Rd man/filter_clinical.Rd man/filter_nsig.Rd man/format_dl_annot.Rd man/format_query_res.Rd man/format_ridge_annot.Rd man/format_up_annot.Rd man/format_up_custom.Rd man/from_crossmeta.Rd man/get_10x_whitepath.Rd man/get_ambience.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_dist.Rd man/get_dprimes.Rd man/get_drug_paths.Rd man/get_drugbank.Rd man/get_drugs_table.Rd man/get_exclude_dirs.Rd man/get_founder.Rd man/get_genego.Rd man/get_gonames.Rd man/get_group_levels.Rd man/get_label_transfer_choices.Rd man/get_mds.Rd man/get_metric_choices.Rd man/get_metric_features.Rd man/get_nearest_row.Rd man/get_npc_choices.Rd man/get_open_a.Rd man/get_palette.Rd man/get_path_df.Rd man/get_path_res.Rd man/get_pred_annot.Rd man/get_presto_markers.Rd man/get_query_cols.Rd man/get_resoln_name.Rd man/get_ridge_data.Rd man/get_sc_dataset_choices.Rd man/get_species.Rd man/get_top.Rd man/get_top_cors.Rd man/get_tsne_coords.Rd man/get_wikipedia.Rd man/handle_sc_progress.Rd man/html_space.Rd man/id_from_tab.Rd man/identify_sc_files.Rd man/init_dseqr.Rd man/integrate_saved_scseqs.Rd man/integrate_scseqs.Rd man/interpret.Rd man/isTruthyAll.Rd man/is_invertible.Rd man/justifiedButtonGroup.Rd man/keep_curr_selected.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_resoln.Rd man/load_scseq_datasets.Rd man/load_scseq_qcgenes.Rd man/load_scseq_qs.Rd man/load_scseq_subsets.Rd man/merge_linkouts.Rd man/navbar2UI.Rd man/navbarUI.Rd man/normalize_scseq.Rd man/plot_biogps.Rd man/plot_cluster.Rd man/plot_dprimes.Rd man/plot_feature.Rd man/plot_feature_sample.Rd man/plot_scseq_dprimes.Rd man/plotlyMDS.Rd man/process_raw_scseq.Rd man/qread.safe.Rd man/query_budger.Rd man/query_drugs.Rd man/remove_bulk_anals.Rd man/remove_dataset_files.Rd man/rightClickMenu.Rd man/run_custom_query.Rd man/run_drug_queries.Rd man/run_dseqr.Rd man/run_fastmnn.Rd man/run_harmony.Rd man/run_integrate_saved_scseqs.Rd man/run_kallisto_scseq.Rd man/run_kallisto_scseq_commands.Rd man/run_limma_scseq.Rd man/run_pca.Rd man/run_post_cluster.Rd man/run_reduction.Rd man/run_scseq_qc.Rd man/save_bulk_anals.Rd man/save_lmfit.Rd man/save_scseq_args.Rd man/save_scseq_data.Rd man/scPage.Rd man/scPageUI.Rd man/sc_dl_filename.Rd man/scseq_part_path.Rd man/selectedAnalInput.Rd man/selectedDrugStudyInput.Rd man/selectedPertSignatureInput.Rd man/shorten_cluster_labels.Rd man/sort_query_table_clin.Rd man/standardize_cellranger.Rd man/subset_saved_scseq.Rd man/summarise_query_table.Rd man/summarize_compound.Rd man/tabPane.Rd man/theme_dimgray.Rd man/theme_no_xaxis.Rd man/theme_no_yaxis.Rd man/theme_pubr.Rd man/transfer_prev_annot.Rd man/transition_efs.Rd man/update_feature_plot.Rd man/validate_custom_query.Rd man/validate_integration.Rd man/validate_metric.Rd man/validate_pdata.Rd man/validate_preds.Rd man/validate_up_annot.Rd man/validate_up_custom.Rd
merge_master.sh
renv.lock
renv/.gitignore
renv/activate.R run_test.R tests/testthat.R tests/testthat/test_calcx.R tests/testthat/test_linkouts.R tests/testthat/test_summarize_compound.R
hms-dbmi/drugseqr documentation built on July 19, 2021, 1:10 p.m.