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:Mahmoud Ahmed [aut, cre]

cRegulome_0.3.2.tar.gz
cRegulome_0.3.2.zip(r-4.6)cRegulome_0.3.2.zip(r-4.5)cRegulome_0.3.2.zip(r-4.4)
cRegulome_0.3.2.tgz(r-4.5-any)cRegulome_0.3.2.tgz(r-4.4-any)
cRegulome_0.3.2.tar.gz(r-4.6-any)cRegulome_0.3.2.tar.gz(r-4.5-any)
cRegulome_0.3.2.tgz(r-4.4-emscripten)
cRegulome.pdf |cRegulome.html✨
cRegulome/json (API)
NEWS

# Install 'cRegulome' in R:

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

Reviews:rOpenSci Software Review #149

Bug tracker:https://github.com/ropensci/cregulome/issues

Pkgdown site:https://docs.ropensci.org

On CRAN:

cancer-genomics database datascience microrna peer-reviewed tcga-data transcription-factors

3.69 score 3 stars 54 scripts 26 downloads 3 mentions 17 exports 57 dependencies

Last updated 5 years agofrom:b3d7fba6f3 (on master). Checks:2 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Total time
pkgdown docs	ERROR	393
source / vignettes	ERROR	249
linux-devel	WARNING	219
linux-release	WARNING	201
macos-release-arm64	WARNING	90
macos-oldrel-arm64	WARNING	101
windows-devel	WARNING	222
windows-release	WARNING	258
windows-oldrel	WARNING	233
wasm-release	OK	321
wasm-oldrel	OK	444

Exports:cmicroRNA cor_hist cor_igraph cor_joy cor_plot cor_prep cor_tidy cor_upset cor_venn_diagram cTF get_db get_mir get_tf stat_collect stat_collect_targets stat_make stat_make_targets

Dependencies:askpass bit bit64 blob cachem cli cpp11 curl DBI fansi farver fastmap formatR futile.logger futile.options ggplot2 ggridges glue gridExtra gtable httr igraph isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix memoise mgcv mime nlme openssl pillar pkgconfig plogr plyr R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp rlang RSQLite scales sys tibble UpSetR utf8 vctrs VennDiagram viridisLite withr

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

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