drugfindR
This is the development version of drugfindR; for the stable release version, see drugfindR.
Investigate iLINCS for candidate repurposable drugs
Bioconductor version: Development (3.24)
This package provides a convenient way to access the LINCS Signatures available in the iLINCS database. These signatures include Consensus Gene Knockdown Signatures, Gene Overexpression signatures and Chemical Perturbagen Signatures. It also provides a way to enter your own transcriptomic signatures and identify concordant and discordant signatures in the LINCS database.
Author: Ali Sajid Imami [aut, cre]
, Smita Sahay [aut]
, Justin Fortune Creeden [aut]
, Robert Erne McCullumsmith [ctb, fnd]
Maintainer: Ali Sajid Imami <Ali.Sajid.Imami at gmail.com>
citation("drugfindR")):
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("drugfindR")
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("drugfindR")| drugfindR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, FunctionalPrediction, GeneSetEnrichment, Network, SingleCell, Software |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | tibble, rlang, dplyr, purrr, readr, stringr, stats, lifecycle, S4Vectors, httr2, curl, DFplyr |
| System Requirements | |
| URL | https://github.com/CogDisResLab/drugfindR https://cogdisreslab.github.io/drugfindR/ |
| Bug Reports | https://github.com/CogDisResLab/drugfindR/issues |
See More
| Suggests | AnnotationDbi, BiocStyle, biocthis, codemetar, devtools, here, httptest2, jsonlite, knitr, rmarkdown, testthat (>= 3.0.0), tidyverse, usethis |
| 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 | drugfindR_1.1.0.tar.gz |
| Windows Binary (x86_64) | drugfindR_1.1.0.zip |
| macOS Binary (big-sur-x86_64) | drugfindR_1.1.0.tgz |
| macOS Binary (sonoma-arm64) | drugfindR_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/drugfindR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/drugfindR |
| Bioc Package Browser | https://code.bioconductor.org/browse/drugfindR/ |
| Package Short Url | https://bioconductor.org/packages/drugfindR/ |
| Package Downloads Report | Download Stats |