Package: DFD 0.1.0

DFD: Extract Drugs from Differential Expression Data

Extract Drugs from Differential Expression Data using the Connectivity Map (CMAP) Approach and Library of Integrated Network-Based Cellular Signatures (LINCS) Database.

Authors:Mohamed Soudy [aut, cre]

DFD_0.1.0.tar.gz

DFD_0.1.0.tar.gz(r-4.5-noble)DFD_0.1.0.tar.gz(r-4.4-noble)
DFD_0.1.0.tgz(r-4.4-emscripten)DFD_0.1.0.tgz(r-4.3-emscripten)
DFD.pdf |DFD.html✨
DFD/json (API)

# Install 'DFD' in R:

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

Bug tracker:https://github.com/mohmedsoudy/dfd/issues

On CRAN:

6 exports 1 stars 0.93 score 183 dependencies 196 downloads

Last updated 11 months agofrom:d9b4a857c7. Checks:OK: 1 NOTE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-linux	NOTE	Sep 05 2024

Exports:convert_id filter_drugs get_drugs prepare_ids read_id run_pipeline

Dependencies:abind affy affyio annotate AnnotationDbi AnnotationHub ape aplot askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob bslib cachem cli clipr clusterProfiler codetools colorspace cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest DOSE dplyr enrichplot evaluate ExperimentHub fansi farver fastmap fastmatch fgsea filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggtree glue GO.db GOSemSim gprofiler2 graph graphlayouts gridExtra gridGraphics GSEABase gson gtable HDF5Array highr hms htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl org.Hs.eg.db patchwork pillar pkgconfig plogr plotly plyr png polyclip preprocessCore prettyunits progress promises purrr qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reactome.db readr reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales scatterpie shadowtext signatureSearch signatureSearchData snow SparseArray statmod stringi stringr SummarizedExperiment sys systemfonts tibble tidygraph tidyr tidyselect tidytree tinytex treeio tweenr tzdb UCSC.utils utf8 vctrs viridis viridisLite visNetwork vroom withr xfun XML xtable XVector yaml yulab.utils zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert Gene Symbols to ENTREZ IDs	convert_id
Re-rank drugs based on the number of targets	filter_drugs
Get Drugs associated with the differential expression profile	get_drugs
Prepare IDs for CMAP Search	prepare_ids
Read Gene IDs from CSV file	read_id
Run the main pipeline for getting drugs from differentail expression profile	run_pipeline