Package: kinograte 0.0.2.9000

Khaled Alganem

kinograte: Kinograte: Netwrok-based multi-omics Integration

Netwrok-based multi-omics integration using a prize-collecting Steiner forest (PCSF) algorithm.

Authors:Khaled Alganem [aut, cre]

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kinograte.pdf |kinograte.html✨
kinograte/json (API)

# Install 'kinograte' in R:

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

Bug tracker:https://github.com/cogdisreslab/kinograte/issues

Datasets:

kinomics_exmaple - An example of Kinome data
ppi_network_example - An example of ppi network
proteomics_exmaple - An example of proteomics data
rnaseq_example - An example of RNA differential gene expression data

On CRAN:

1.70 score 2 scripts 8 exports 109 dependencies

Last updated 3 years agofrom:28859ba6f5. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 20 2024
R-4.5-win	WARNING	Nov 20 2024
R-4.5-linux	WARNING	Nov 20 2024
R-4.4-win	WARNING	Nov 20 2024
R-4.4-mac	WARNING	Nov 20 2024
R-4.3-win	WARNING	Nov 20 2024
R-4.3-mac	WARNING	Nov 20 2024

Exports:%>%combine_scores kinograte network_enrichment percentile_rank score_plot top_hits visualize_network

Dependencies:AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics Biostrings bit bit64 blob broom bslib cachem cli colorspace commonmark corrplot countrycode cpp11 crayon curl DBI digest dplyr echarts4r evaluate fansi farver fastmap fontawesome fs generics GenomeInfoDb GenomeInfoDbData ggplot2 glue GO.db graph gtable highr htmltools htmlwidgets httpuv httr igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling later lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime munsell nlme openssl org.Hs.eg.db PCSF pillar pkgconfig plogr png promises purrr R6 rappdirs RColorBrewer Rcpp reactable reactR rlang rmarkdown RSQLite rstudioapi S4Vectors sass scales shiny sourcetools SparseM stringi stringr sys tibble tidyr tidyselect tinytex topGO UCSC.utils utf8 vctrs viridisLite visNetwork withr xfun xtable XVector yaml zlibbioc

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
Combines standardized scores	combine_scores
Integrate omic datasets using PCSF	kinograte
an example of Kinome data	kinomics_exmaple
Network pathway analysis	network_enrichment
Ranks genes/proteins using a percentile ranking for a selected variable	percentile_rank
an example of ppi network	ppi_network_example
an example of proteomics data	proteomics_exmaple
an example of RNA differential gene expression data	rnaseq_example
Plot the normalized score	score_plot
Extracts top hits (genes/proteins) based on the normalized score	top_hits
Visualize integrated network	visualize_network

Usage by other packages (reverse dependencies)