Package: BloodCancerMultiOmics2017 1.33.0

Małgorzata Oleś

BloodCancerMultiOmics2017: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oleś M, Lu J et al. - experimental data and complete analysis

The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oleś M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801.

Authors:Małgorzata Oleś, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber

BloodCancerMultiOmics2017_1.33.0.tar.gz
BloodCancerMultiOmics2017_1.33.0.tar.gz(r-4.7-any)BloodCancerMultiOmics2017_1.33.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BloodCancerMultiOmics2017/json (API)

# Install 'BloodCancerMultiOmics2017' in R:
install.packages('BloodCancerMultiOmics2017', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • conctab - Concentrations of drugs used in the drug screen
  • cytokineViab - Response of CLL to exposure to cytokines
  • day23rep - Cell viability data for 3 replicated samples
  • dds - Gene expression data
  • drpar - Cell viability data from the high-throughput drug screen
  • drugs - Meta data of the compounds
  • exprTreat - Gene expression before and after drug treatment
  • lpdAll - An assembly of drug viability data, methylation clusters, important mutations and copy number variants
  • methData - DNA methylation data
  • mutCOM - Genetic information of patient samples
  • patmeta - Meta data of the patient samples
  • validateExp - Data of the validation drug sensitivity screen using five additional drugs

On BioConductor:BloodCancerMultiOmics2017-1.33.0(data/experiment 3.24)BloodCancerMultiOmics2017-1.32.0(data/experiment 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

experimentdatareproducibleresearchcancerdataleukemiacancerdatadatapkg

4.52 score 11 scripts 19 exports 146 dependencies

Last updated from:852576d3c6. Checks:1 ERROR, 2 WARNING, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR265
linux-develWARNING468
source / vignettesOK1605
linux-releaseWARNING404

Exports:addNriskcol2hexdeckeldefineResponseGroupsexp10divgiveDrugLabellog10divmeltWholeDFmoroundnriskpercentAxisScalepheatmapwhsafeMatchscientific_10smunliststripConcsurvplottoCapswhichInGrob

Dependencies:abindaskpassbase64encbeeswarmBHBiobaseBiocGenericsBiocParallelbrewbriobslibcachemcallrclicliprcodetoolscommonmarkcpp11crayoncredentialscurlDelayedArraydescDESeq2devtoolsdiffobjdigestdownlitdplyrellipsisevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesgertggdendroggplot2gitcredsglmnetgluegtablehighrhtmltoolshtmlwidgetshttpuvhttr2iniipflassoIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUIopensslotelpakpillarpkgbuildpkgconfigpkgdownpkgloadplyrpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppRcppArmadilloRcppEigenrdtoolsreshape2rlangrmarkdownroxygen2rprojrootrstudioapirversionsS4ArraysS4VectorsS7sassscalesSeqinfosessioninfoshapeshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsurvivalsyssystemfontstestthattextshapingtibbletidyselecttinytexurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunxml2xopenxtableXVectoryamlzip

BloodCancerMultiOmics2017 - complete analysis
Introduction | End of session
Rendered fromBloodCancerMultiOmics2017.Rmdusingknitr::rmarkdown

Last update: 2025-04-08
Started: 2018-01-26

BloodCancerMultiOmics2017 - data overview
Prerequisites | Introduction | Data overview | Patient metadata | High-throughput drug screen data | Gene mutation data | Gene expression data | DNA methylation data | Other | Original data | Session info
Rendered fromBloodCancerMultiOmics2017-dataOverview.Rmdusingknitr::rmarkdown

Last update: 2019-11-24
Started: 2018-01-26

Readme and manuals

Help Manual

Help pageTopics
Add number-at-risk annotations to a plotaddNrisk
Converts color names with alpha to hexcol2hex
Concentrations of drugs used in the drug screenconctab
Response of CLL to exposure to cytokinescytokineViab
Cell viability data for 3 replicated samplesday23rep
Gene expression datadds
treshold an array from below and abovedeckel
divides patients into response groups: BTK, MEK, mTOR, non-respondersdefineResponseGroups
Cell viability data from the high-throughput drug screendrpar
Meta data of the compoundsdrugs
Axis labels for p-valuesexp10div
Gene expression before and after drug treatmentexprTreat
Convert extended drug IDs to drug namesgiveDrugLabel
log10 with signlog10div
An assembly of drug viability data, methylation clusters, important mutations and copy number variantslpdAll
Wide format to long format data conversionmeltWholeDF
DNA methylation datamethData
Round numbers to the ceiling of a given basemoround
Genetic information of patient samplesmutCOM
Get number-at-risk from a survfit objectnrisk
Meta data of the patient samplespatmeta
Fraction to percent converterpercentAxisScale
A modification of 'pheatmap' from the pheatmap package by Raivo Kolde: draw clustered heatmaps.pheatmapwh
safe version of the match function that throws an error if there is no matchsafeMatch
log10 scale labels in ggplot2scientific_10
Unlist with name preservationsmunlist
Convert extended drug IDs to drug namesstripConc
Draw augmented K-M survival curvessurvplot
Capitalize first charactertoCaps
Data of the validation drug sensitivity screen using five additional drugsvalidateExp
Return indices of layers of interest from the grob objectwhichInGrob