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
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cRegulome_0.3.2.tgz(r-4.4-any)cRegulome_0.3.2.tgz(r-4.3-any)
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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'))

Peer review:

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

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

On CRAN:

cancer-genomicsdatabasedatasciencemicrornapeer-reviewedtcga-datatranscription-factors

3.69 score 3 stars 54 scripts 55 downloads 3 mentions 17 exports 59 dependencies

Last updated 5 years agofrom:b3d7fba6f3 (on master). Checks:1 ERROR, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesFAILJan 03 2025
R-4.5-winWARNINGJan 03 2025
R-4.5-linuxWARNINGJan 03 2025
R-4.4-winWARNINGJan 03 2025
R-4.4-macWARNINGJan 03 2025
R-4.3-winWARNINGJan 03 2025
R-4.3-macWARNINGJan 03 2025

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

Citation

Ahmed M, Kim DR. 2019. cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer. PeerJ 7:e6509 https://doi.org/10.7717/peerj.6509

Corresponding BibTeX entry:

  @Article{,
    title = {cRegulome: an R package for accessing microRNA and
      transcription factor-gene expression correlations in cancer},
    author = {Mahmoud Ahmed and Deok Ryong Kim},
    year = {2019},
    journal = {PeerJ},
    doi = {10.7717/peerj.6509},
    volume = {7},
    pages = {e6509},
  }