Package: omicRexposome 1.35.0

Xavier Escribà Montagut

omicRexposome: Exposome and omic data associatin and integration analysis

omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).

Authors:Carles Hernandez-Ferrer [aut, cre], Juan R. González [aut]

omicRexposome_1.35.0.tar.gz
omicRexposome_1.35.0.zip(r-4.7)omicRexposome_1.35.0.zip(r-4.6)omicRexposome_1.35.0.zip(r-4.5)
omicRexposome_1.35.0.tgz(r-4.6-any)omicRexposome_1.35.0.tgz(r-4.5-any)
omicRexposome_1.35.0.tar.gz(r-4.7-any)omicRexposome_1.35.0.tar.gz(r-4.6-any)
omicRexposome_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
omicRexposome/json (API)

# Install 'omicRexposome' in R:

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

Datasets:

asr - 'ResultSet' for testing and illustration purpouses
crs - 'ResultSet' for testing and illustration purpouses
mds - 'MultiDataSet' for testing and illustration purpouses

On BioConductor:omicRexposome-1.35.0(bioc 3.24)omicRexposome-1.34.0(bioc 3.23)

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

immunooncology workflowstep multiplecomparison visualization geneexpression differentialexpression differentialmethylation generegulation epigenetics proteomics transcriptomics statisticalmethod regression

4.30 score 5 scripts 2 mentions 11 exports 217 dependencies

Last updated from:2518c92ed5. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	305
linux-devel-x86_64	NOTE	518
source / vignettes	OK	683
linux-release-x86_64	NOTE	529
macos-release-arm64	NOTE	386
macos-oldrel-arm64	NOTE	268
windows-devel	NOTE	516
windows-release	NOTE	350
windows-oldrel	NOTE	420
wasm-release	OK	299

Exports:add_cls add_exp association crossomics getIntegration plotAssociation plotHits plotIntegration plotLambda tableHits tableLambda

Dependencies:abind ade4 annotate AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob boot broom bslib cachem calibrate car carData caTools checkmate circlize cli clipr clue cluster codetools colorspace corrplot cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray Deriv digest doBy dplyr DT edgeR ellipse emmeans estimability evaluate FactoMineR farver fastICA fastmap flashClust fontawesome forcats foreach forecast foreign formatR Formula fracdiff fs futile.logger futile.options genefilter generics GenomicRanges ggplot2 ggrepel ggridges glmnet GlobalOptions glue gmm gplots gridExtra gtable gtools haven highr Hmisc hms htmlTable htmltools htmlwidgets httr impute imputeLCMD IRanges irlba isoband isva iterators JADE jomo jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 lmtest locfit lsr made4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mice microbenchmark mime minqa mitml modelr multcompView MultiDataSet mvtnorm nlme nloptr nnet norm numDeriv omicade4 openssl ordinal otel pan pbkrtest pcaMethods pillar pixmap pkgconfig plyr PMA png prettyunits progress promises purrr qqman quantreg qvalue R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas reshape2 rexposome rlang rmarkdown rpart RSpectra RSQLite rstudioapi S4Arrays S4Vectors S7 sandwich sass scales scatterplot3d Seqinfo shape SmartSVA snow sp SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sva sys tibble tidyr tidyselect timeDate tinytex tmvtnorm tzdb ucminf urca utf8 vctrs viridisLite vroom withr xfun XML xtable XVector yaml zoo

Exposome Data Integration with Omic Data

Rendered fromexposome_omic_integration.Rmdusingknitr::rmarkdown

Last update: 2024-02-12
Started: 2017-03-31

Help page	Topics
Method to add an ExposomeClust to a MultiDataSet	add_cls add_cls,MultiDataSet,ExposomeClust-method
Method to add an ExposomeSet to a MultiDataSet	add_exp add_exp,MultiDataSet,ExposomeSet-method
'ResultSet' for testing and illustration purpouses	asr
# -------------------------- Method to perform an association study between transcriptome and exposom	association association,MultiDataSet-method
Function to perform a Transcriptome-Wide Association Study	crossomics crossomics,MultiDataSet-method
'ResultSet' for testing and illustration purpouses	crs
Method to extrat integration-feature result from a ResultSet	getIntegration getIntegration,ResultSet-method
'MultiDataSet' for testing and illustration purpouses	mds
omicRexposome: Package for exposome and omic data associatin and integration	omicRexposome-package omicRexposome
Function to draw de result of an association study	plotAssociation plotAssociation,ResultSet-method
Plot number of hits per result in ResultSet	plotHits plotHits,ResultSet-method
Function to draw de result of an integration study	plotIntegration plotIntegration,ResultSet-method
Plot lambda score for all results in a ResultSet	plotLambda plotLambda,ResultSet-method
Transforms the discrete genotype from a 'snpSet' to a 'matrix' of a continuous variable.	snpToContinuous snpToContinuous,SnpSet-method
Counts the number of hits on the results stored in a ResultSet	tableHits tableHits,ResultSet-method
Compute a lambda score on the results stored in a ResultSet	tableLambda tableLambda,ResultSet-method

Package: omicRexposome 1.35.0

omicRexposome: Exposome and omic data associatin and integration analysis

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