Overview | Bundled Example Data | The disease signature | The siginfo metadata | Use Case 1 — Finding Repurposing Compounds | Filter to compound signatures | Build compound reference matrix | Score the AML signature against compounds | Inspect top compound hits | Annotate compound hits | Barcode heatmap for top compounds | Split-direction heatmap | Use Case 2 — Finding Therapeutic Gene Targets | Filter to gene perturbation signatures | Build gene perturbation reference matrix | Score the AML signature against gene perturbations | Inspect top gene perturbation hits | Annotate gene perturbation hits | Barcode heatmap for top gene perturbations | Split-direction heatmap for gene perturbations | Comparing the Two Use Cases | Comparison to Similar Packages | Running with Full CMap Data | Session Info
Package: CONCERTDR 0.99.2
Hengxin Pan
CONCERTDR: Drug Response Data Analysis Using CMap Database
Provides a complete pipeline for drug repurposing analysis using the Connectivity Map (CMap) L1000 database. Functionality includes database subsetting, reference profile extraction from GCTX files, signature matching via Kolmogorov-Smirnov, GSEA-based, cosine similarity, and other methods, result annotation against CMap compound metadata, z-score matrix extraction, and publication-quality clustermap visualization via ComplexHeatmap. Connectivity scoring methods (KS, GSEA, XCos, XSum, Zhang) are implemented internally based on the algorithms described in Lamb et al. (2006), Subramanian et al. (2005), Cheng et al. (2014), and Zhang & Gant (2008), removing the need for external GitHub-only dependencies.
Authors:
CONCERTDR_0.99.2.tar.gz
CONCERTDR_0.99.2.zip(r-4.7-any)CONCERTDR_0.99.2.zip(r-4.6-any)CONCERTDR_0.99.2.zip(r-4.5-any)
CONCERTDR_0.99.2.tgz(r-4.6-any)CONCERTDR_0.99.2.tgz(r-4.5-any)
CONCERTDR_0.99.2.tar.gz(r-4.7-any)CONCERTDR_0.99.2.tar.gz(r-4.6-any)
CONCERTDR_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CONCERTDR/json (API)
| # Install 'CONCERTDR' in R: |
| install.packages('CONCERTDR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/davidsongroup/concertdr/issues
On BioConductor:CONCERTDR-0.99.2(bioc 3.24)
geneexpressionpharmacogenomicssoftwaretranscriptomicsdataimport
Last updated from:d27d37cc7c. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 150 | ||
| linux-devel | OK | 249 | ||
| source / vignettes | OK | 206 | ||
| linux-release | OK | 273 | ||
| macos-release | OK | 178 | ||
| macos-oldrel | OK | 173 | ||
| windows-devel | OK | 166 | ||
| windows-release | OK | 164 | ||
| windows-oldrel | OK | 169 | ||
| wasm-release | OK | 112 |
Exports:annotate_drug_resultscreate_signature_from_gene_listsextract_cmap_data_from_siginfoextract_compound_idextract_signature_zscoresfuzzy_drug_matchplot_signature_direction_tile_barcodeprocess_combinations_fileprocess_signature_with_dfsubset_siginfo_beta
Dependencies:biocmakedata.tabledir.expiryfilelockrhdf5rhdf5filtersRhdf5lib
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate CONCERTDR Results with Drug Information | annotate_drug_results |
| Create a Signature Data Frame from Gene Lists | create_signature_from_gene_lists |
| Extract CMap Data Using Siginfo File Directly | extract_cmap_data_from_siginfo |
| Extract Compound ID from Signature Matching Results | extract_compound_id |
| Extract z-score matrix for barcode heatmap | extract_signature_zscores |
| Fuzzy String Matching for Drug Names | fuzzy_drug_match |
| Plot 2D Barcode Heatmap from GCTX (Single Drug Context) | plot_signature_direction_tile_barcode |
| Plot method for cmap_signature_result objects | plot.cmap_signature_result |
| Print method for cmap_signature_result objects | print.cmap_signature_result |
| Process Multiple Combinations of Time, Dose, and Cell Line | process_combinations_file |
| Process drug response signatures against reference data in a dataframe | process_signature_with_df |
| Subset siginfo_beta file interactively with smart preview | subset_siginfo_beta |
| Summary method for cmap_signature_result objects | summary.cmap_signature_result |