Package: gINTomics 1.3.0

Angelo Velle

gINTomics: Multi-Omics data integration

gINTomics is an R package for Multi-Omics data integration and visualization. gINTomics is designed to detect the association between the expression of a target and of its regulators, taking into account also their genomics modifications such as Copy Number Variations (CNV) and methylation. What is more, gINTomics allows integration results visualization via a Shiny-based interactive app.

Authors:Angelo Velle [cre, aut], Francesco Patane' [aut], Chiara Romualdi [aut]

gINTomics_1.3.0.tar.gz
gINTomics_1.3.0.zip(r-4.5)gINTomics_1.3.0.zip(r-4.4)gINTomics_1.1.0.zip(r-4.3)
gINTomics_1.3.0.tgz(r-4.4-any)gINTomics_1.1.0.tgz(r-4.3-any)
gINTomics_1.3.0.tar.gz(r-4.5-noble)gINTomics_1.3.0.tar.gz(r-4.4-noble)
gINTomics_1.3.0.tgz(r-4.4-emscripten)gINTomics_1.1.0.tgz(r-4.3-emscripten)
gINTomics.pdf |gINTomics.html✨
gINTomics/json (API)
NEWS

# Install 'gINTomics' in R:

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

Bug tracker:https://github.com/angelovelle96/gintomics/issues

Datasets:

mirna_hsa - MiRNA IDs. Dataset containing lastly definition of miRNAs (Names, Accessions, Sequences, Families and others) from different miRBase versions (From miRBase version 6 to version 22).
mmultiassay_ov - Example data for a standard workflow. This is an example dataset containing a MultiAssayExperiment of 20 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. The object contains all the available input data types: Gene expression data, miRNA expression data, gene methylation data, gene Copy Number Variations and miRNA Copy Number Variations.

On BioConductor:gINTomics-1.3.0(bioc 3.21)gINTomics-1.2.0(bioc 3.20)

geneexpression rnaseq microarray visualization copynumbervariation genetarget

5.41 score 3 stars 3 scripts 76 downloads 18 exports 229 dependencies

Last updated 2 months agofrom:3ba788eebd. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	WARNING	Sep 30 2024
R-4.3-mac	WARNING	Sep 30 2024

Exports:create_multiassay dot_plotly extract_model_res plot_chr_distribution plot_heatmap plot_network plot_ridge plot_tf_distribution plot_venn plot_volcano run_cnv_integration run_genomic_enrich run_genomic_integration run_met_integration run_multiomics run_shiny run_tf_enrich run_tf_integration

Dependencies:abind AnnotationDbi ape aplot askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib cachem callr cellranger checkmate circlize cli clipr clisymbols clue cluster clusterProfiler codetools colorspace commonmark ComplexHeatmap cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest doParallel DOSE dplyr DT edgeR enrichplot evaluate fansi farver fastmap fastmatch fgsea filelock fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggridges ggtangle ggtree ggvenn GlobalOptions glue GO.db GOSemSim graph graphite graphlayouts gridExtra gridGraphics gson gtable gtools highr hms htmltools htmlwidgets httpuv httr httr2 igraph InteractiveComplexHeatmap IRanges isoband iterators jquerylib jsonlite kableExtra KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit logger lubridate magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime MultiAssayExperiment munsell nlme OmnipathR openssl org.Hs.eg.db org.Mm.eg.db patchwork pillar pkgconfig plogr plotly plyr png polyclip prettyunits processx progress promises ps purrr qvalue R.methodsS3 R.oo R.utils R6 randomForest rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reactome.db ReactomePA readr readxl rematch reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rstudioapi rtracklayer rvest S4Arrays S4Vectors sass scales scatterpie selectr shape shiny shiny.gosling shiny.react shinydashboard snow sourcetools SparseArray statmod stringi stringr SummarizedExperiment svglite sys systemfonts tibble tidygraph tidyr tidyselect tidytree timechange tinytex treeio tweenr TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene tzdb UCSC.utils utf8 vctrs viridis viridisLite visNetwork vroom withr xfun XML xml2 xtable XVector yaml yulab.utils zip zlibbioc

gINTomics vignette

Angelo Velle, Francesco Patanè, Chiara Romualdi

Rendered fromgINTomics.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-04-04
Started: 2023-07-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
MultiAssayExperiment generation	create_multiassay
plotting enrichment	dot_plotly
Setting method for extracting results	extract_model_res extract_model_res,list-method extract_model_res,MultiClass-method extract_model_res,MultiOmics-method
miRNA IDs. Dataset containing lastly definition of miRNAs (Names, Accessions, Sequences, Families and others) from different miRBase versions (From miRBase version 6 to version 22).	mirna_hsa
Example data for a standard workflow. This is an example dataset containing a MultiAssayExperiment of 20 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. The object contains all the available input data types: Gene expression data, miRNA expression data, gene methylation data, gene Copy Number Variations and miRNA Copy Number Variations.	mmultiassay_ov
MultiClass Class	MultiClass-class
MultiOmics Class	MultiOmics-class
plotting chr distribution	plot_chr_distribution
plotting heatmap	plot_heatmap
Plotting network	plot_network
plotting ridge	plot_ridge
plotting TF distribution	plot_tf_distribution
plotting venn	plot_venn
plotting volcano	plot_volcano
Integration of expression and Copy Number Variations	run_cnv_integration
Running genomic enrichment analysis	run_genomic_enrich
Integration of expression, Copy Number Variations and methylation data	run_genomic_integration
Integration of expression and methylation	run_met_integration
Complete Multi-Omics integration	run_multiomics
Start a Shiny application for integrated multi-omics data analysis.	run_shiny
Running TF enrichment analysis	run_tf_enrich
Integration of expression and Transcription Factors / Generic Regulators	run_tf_integration