Package: drugfindR 0.99.657

Ali Sajid Imami

drugfindR: Investigate iLINCS for candidate repurposable drugs

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.

Authors:Ali Sajid Imami [aut, cre], Justin Fortune Creeden [aut], Evelyn Alden Bates [aut], Smita Sahay [aut]

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drugfindR/json (API)
NEWS

# Install drugfindR in R:

install.packages('drugfindR', repos = c('https://cogdisreslab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cogdisreslab/drugfindr/issues

On CRAN:

lincs ilincs drug repurposing drug discovery transcriptomics gene expression gene knockdown gene overexpression chemical perturbagen drugfindr bioinformatics bioinformatics-pipeline

7 exports 7 stars 1.85 score 39 dependencies

Last updated 10 days agofrom:dbbb832f42dba500ecccb10fd108d197243a81f3

Exports:consensusConcordants filterSignature getConcordants getSignature investigateSignature investigateTarget prepareSignature

Dependencies:askpass BiocGenerics bit bit64 cli clipr cpp11 crayon curl dplyr fansi generics glue hms httr jsonlite lifecycle magrittr mime openssl pillar pkgconfig prettyunits progress purrr R6 readr rlang S4Vectors stringi stringr sys tibble tidyselect tzdb utf8 vctrs vroom withr

drugfindR

Rendered fromdrugfindR.Rmdusingknitr::rmarkdownon Jun 17 2024.

Last update: 2024-06-17
Started: 2023-01-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check if the library is valid	.validateLibrary
Generate a Consensus list of Targets [Experimental]	consensusConcordants
Filter the L1000 Signature [Experimental]	filterSignature
Get Concordant Signatures from iLINCS [Experimental]	getConcordants
Get the L1000 Signature from iLINCS [Experimental]	getSignature
Investigate a given DGE dataset [Experimental]	investigateSignature
Investigate a Given Gene or Drug [Experimental]	investigateTarget
Load the correct metadata table	loadMetadata
Prepare an L1000 Signature froma given differential gene expression output [Experimental]	prepareSignature
Stop if the libraries are invalid	stopIfInvalidLibraries
Rename the Target-Related Columns	targetRename
Check if the libraries input are valid	validateLibraries