Package: drugfindR 0.99.1017

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], Smita Sahay [aut], Justin Fortune Creeden [aut]

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drugfindR.pdf |drugfindR.html✨
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

6.14 score 8 stars 145 scripts 7 exports 38 dependencies

Last updated 16 hours agofrom:8166bac3b2. Checks:6 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 20 2025
R-4.5-win	OK	Feb 20 2025
R-4.5-mac	OK	Feb 20 2025
R-4.5-linux	OK	Feb 20 2025
R-4.4-win	OK	Feb 20 2025
R-4.4-mac	OK	Feb 20 2025

Exports:consensusConcordants filterSignature getConcordants getSignature investigateSignature investigateTarget prepareSignature

Dependencies:askpass BiocGenerics bit bit64 cli clipr cpp11 crayon curl dplyr fansi generics glue hms httr2 lifecycle magrittr openssl pillar pkgconfig prettyunits progress purrr R6 rappdirs readr rlang S4Vectors stringi stringr sys tibble tidyselect tzdb utf8 vctrs vroom withr

drugfindR

Rendered fromdrugfindR.Rmdusingknitr::rmarkdownon Feb 20 2025.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate a Consensus list of Targets [Stable]	consensusConcordants
Filter the L1000 Signature [Stable]	filterSignature
Get Concordant Signatures from iLINCS [Stable]	getConcordants
Get the L1000 Signature from iLINCS [Stable]	getSignature
Investigate a given DGE dataset [Stable]	investigateSignature
Investigate a Given Gene or Drug [Stable]	investigateTarget
Prepare an L1000 Signature froma given differential gene expression output [Stable]	prepareSignature
Rename the Target-Related Columns	targetRename