CONCERTDR
This is the development version of CONCERTDR; to use it, please install the devel version of Bioconductor.
Drug Response Data Analysis Using CMap Database
Bioconductor version: Development (3.24)
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.
Author: Hengxin Pan [aut, cre]
, Chin Wee Tan [aut, ths]
, Gad Abraham [aut, ths], Nadia Davidson [aut, ths]
Maintainer: Hengxin Pan <pan.h at wehi.edu.au>
citation("CONCERTDR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("CONCERTDR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CONCERTDR")| Drug Repurposing with CONCERTDR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, GeneExpression, Pharmacogenomics, Software, Transcriptomics |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | data.table, rhdf5, stats, utils |
| System Requirements | |
| URL | https://github.com/DavidsonGroup/CONCERTDR |
| Bug Reports | https://github.com/DavidsonGroup/CONCERTDR/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle, ComplexHeatmap, circlize, ggplot2, RecordLinkage |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CONCERTDR_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | CONCERTDR_0.99.2.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/CONCERTDR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CONCERTDR |
| Bioc Package Browser | https://code.bioconductor.org/browse/CONCERTDR/ |
| Package Short Url | https://bioconductor.org/packages/CONCERTDR/ |
| Package Downloads Report | Download Stats |