Package: CaDrA 1.5.0
Reina Chau
CaDrA: Candidate Driver Analysis
Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA's main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.
Authors:
CaDrA_1.5.0.tar.gz
CaDrA_1.5.0.zip(r-4.5)CaDrA_1.5.0.zip(r-4.4)CaDrA_1.3.2.zip(r-4.3)
CaDrA_1.5.0.tgz(r-4.4-x86_64)CaDrA_1.5.0.tgz(r-4.4-arm64)CaDrA_1.3.2.tgz(r-4.3-x86_64)CaDrA_1.3.2.tgz(r-4.3-arm64)
CaDrA_1.5.0.tar.gz(r-4.5-noble)CaDrA_1.5.0.tar.gz(r-4.4-noble)
CaDrA_1.5.0.tgz(r-4.4-emscripten)CaDrA_1.3.2.tgz(r-4.3-emscripten)
CaDrA.pdf |CaDrA.html✨
CaDrA/json (API)
NEWS
| # Install 'CaDrA' in R: |
| install.packages('CaDrA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/montilab/cadra/issues
- BRCA_GISTIC_MUT_SIG - Genomic Data from TCGA BRCA MUT + GISTIC
- CCLE_MUT_SCNA - Genomic Data from CCLE MUT + SCNA
- CTNBB1_reporter - Transcriptional Activity of Beta-Catenin in Cancers
- TAZYAP_BRCA_ACTIVITY - YAP/TAZ Activity in TCGA BRCA dataset
- perm_res - Pre-computed permutation results for simulated data
- sim_FS - Simulated Genomic Data
- sim_Scores - Simulated Input Scores
- topn_list - Top-N Results for Simulated Data
On BioConductor:CaDrA-1.5.0(bioc 3.21)CaDrA-1.4.0(bioc 3.20)
microarrayrnaseqgeneexpressionsoftwarefeatureextraction
Last updated 2 months agofrom:3f6af6cc9e. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win-x86_64 | OK | Nov 29 2024 |
| R-4.5-linux-x86_64 | OK | Nov 29 2024 |
| R-4.4-win-x86_64 | OK | Nov 29 2024 |
| R-4.4-mac-x86_64 | OK | Nov 29 2024 |
| R-4.4-mac-aarch64 | OK | Nov 29 2024 |
| R-4.3-win-x86_64 | OK | Sep 24 2024 |
| R-4.3-mac-x86_64 | OK | Sep 24 2024 |
| R-4.3-mac-aarch64 | OK | Sep 24 2024 |
Exports:CaDrAcalc_rowscorecandidate_searchgenerate_permutationsmeta_plotpermutation_plotprefilter_datatopn_besttopn_plot
Dependencies:abindaskpassBiobaseBiocGenericsbitopscaToolsclicodetoolscolorspacecrayoncurlDelayedArraydigestdoParallelfansifarverforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshttrIRangesisobanditeratorsjsonliteKernSmoothknnmilabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemisc3dmunsellnlmeopensslpillarpkgconfigplyrppcorR.cacheR.methodsS3R.ooR.utilsR6RColorBrewerRcppreshape2rlangS4ArraysS4VectorsscalesSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
How to run CaDrA within a Docker Environment
Rendered fromdocker.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-03-14
Started: 2023-12-12
Permutation-Based Testing
Rendered frompermutation_based_testing.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-03-14
Started: 2022-07-10
Scoring Functions
Rendered fromscoring_functions.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-09-21
Started: 2022-07-10
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Genomic Data from TCGA BRCA MUT + GISTIC | BRCA_GISTIC_MUT_SIG |
| CaDrA Search | CaDrA |
| Calculate row-wise scores of a given binary feature set based on a given scoring method | calc_rowscore |
| Candidate Search | candidate_search |
| Genomic Data from CCLE MUT + SCNA | CCLE_MUT_SCNA |
| Transcriptional Activity of Beta-Catenin in Cancers | CTNBB1_reporter |
| Random permutation matrix generator | generate_permutations |
| Candidate Drivers Search Plot | meta_plot |
| Pre-computed permutation results for simulated data ('sim_FS') | perm_res |
| Permutation Best Scores Plot | permutation_plot |
| Pre-filter features | prefilter_data |
| Simulated Genomic Data | sim_FS |
| Simulated Input Scores | sim_Scores |
| YAP/TAZ Activity in TCGA BRCA dataset | TAZYAP_BRCA_ACTIVITY |
| Top 'N' Best Meta-Features | topn_best |
| Top-N Results for Simulated Data ('sim_FS') | topn_list |
| Top 'N' Plot | topn_plot |
