Package: cRegulome 0.3.2
Mahmoud Ahmed
cRegulome: Obtain and Visualize Regulome-Gene Expression Correlations in Cancer
Builds a 'SQLite' database file of pre-calculated transcription factor/microRNA-gene correlations (co-expression) in cancer from the Cistrome Cancer Liu et al. (2011) <doi:10.1186/gb-2011-12-8-r83> and 'miRCancerdb' databases (in press). Provides custom classes and functions to query, tidy and plot the correlation data.
Authors:
cRegulome_0.3.2.tar.gz
cRegulome_0.3.2.zip(r-4.5)cRegulome_0.3.2.zip(r-4.4)cRegulome_0.3.2.zip(r-4.3)
cRegulome_0.3.2.tgz(r-4.4-any)cRegulome_0.3.2.tgz(r-4.3-any)
cRegulome_0.3.2.tar.gz(r-4.5-noble)cRegulome_0.3.2.tar.gz(r-4.4-noble)
cRegulome_0.3.2.tgz(r-4.4-emscripten)cRegulome_0.3.2.tgz(r-4.3-emscripten)
cRegulome.pdf |cRegulome.html✨
cRegulome/json (API)
NEWS
| # Install 'cRegulome' in R: |
| install.packages('cRegulome', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ropensci/cregulome/issues
cancer-genomicsdatabasedatasciencemicrornapeer-reviewedtcga-datatranscription-factors
Last updated 5 years agofrom:b3d7fba6f3 (on master). Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 18 2024 |
| R-4.5-win | NOTE | Sep 18 2024 |
| R-4.5-linux | NOTE | Sep 18 2024 |
| R-4.4-win | OK | Sep 18 2024 |
| R-4.4-mac | OK | Sep 18 2024 |
| R-4.3-win | OK | Sep 18 2024 |
| R-4.3-mac | OK | Sep 18 2024 |
Exports:cmicroRNAcor_histcor_igraphcor_joycor_plotcor_prepcor_tidycor_upsetcor_venn_diagramcTFget_dbget_mirget_tfstat_collectstat_collect_targetsstat_makestat_make_targets
Dependencies:askpassbitbit64blobcachemclicolorspacecpp11curlDBIfansifarverfastmapformatRfutile.loggerfutile.optionsggplot2ggridgesgluegridExtragtablehttrigraphisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrR.methodsS3R.ooR.utilsR6RColorBrewerRcpprlangRSQLitescalessystibbleUpSetRutf8vctrsVennDiagramviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Construct cmicroRNA object | cmicroRNA |
| A histogram of the correlations of microRNA or tf sets | cor_hist |
| Make an igraph object | cor_igraph |
| A joy plot of correlation of microRNA or tf sets | cor_joy |
| Plot method for cmicroRNA and cTF objects | cor_plot |
| Prepare correlation data for plotting | cor_prep |
| Tidy cmicroRNA and cTF objects | cor_tidy |
| 'upset' plot of microRNA or tf sets | cor_upset |
| Venn Diagram of microRNA or transcription factor correlated features | cor_venn_diagram |
| 'cRegulome' package | cRegulome |
| Construct cTF object | cTF |
| Get cRegulome.db file | get_db |
| Get microRNA correlations from cRegulome.db | get_mir |
| Get transcription factor correlations from cRegulome.db | get_tf |
| Collect data from SQLite database | stat_collect |
| Collect target features from SQLite database | stat_collect_targets |
| Make A SQL statement | stat_make |
| Make A SQL statement to extract target features | stat_make_targets |
