Package: romic 1.1.3

romic: R for High-Dimensional Omic Data

Represents high-dimensional data as tables of features, samples and measurements, and a design list for tracking the meaning of individual variables. Using this format, filtering, normalization, and other transformations of a dataset can be carried out in a flexible manner. 'romic' takes advantage of these transformations to create interactive 'shiny' apps for exploratory data analysis such as an interactive heatmap.

Authors:Sean Hackett [aut, cre], Calico Life Sciences LLC [cph, fnd]

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romic.pdf |romic.html✨
romic/json (API)
NEWS

# Install 'romic' in R:

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

Datasets:

brauer_2008 - Brauer 2008
brauer_2008_tidy - Brauer 2008
brauer_2008_triple - Brauer 2008

On CRAN:

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

2.70 score 1 stars 10 scripts 163 downloads 54 exports 72 dependencies

Last updated 1 years agofrom:3aa20f3903. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 15 2024
R-4.5-win	NOTE	Oct 15 2024
R-4.5-linux	NOTE	Oct 15 2024
R-4.4-win	NOTE	Oct 15 2024
R-4.4-mac	NOTE	Oct 15 2024
R-4.3-win	OK	Oct 15 2024
R-4.3-mac	OK	Oct 15 2024

Exports:add_pcs app_flow app_heatmap app_pcs center_tomic check_tomic convert_wide_to_tidy_omic create_tidy_omic create_triple_omic export_tomic_as_tidy export_tomic_as_triple export_tomic_as_wide filter_tomic filterInput filterServer format_names_for_plotting get_design_tbl get_tomic_table ggBivOutput ggBivServer ggplotOutput ggplotServer ggUnivOutput ggUnivServer hclust_order impute_missing_values lassoInput lassoServer organizeInput organizeServer plot_bivariate plot_heatmap plot_univariate plotsaverInput plotsaverServer remove_missing_values shiny_filter_test shiny_ggbiv_test shiny_ggplot_test shiny_gguniv_test shiny_lasso_test shiny_lasso_test_reactval shiny_organize_test shiny_plotsaver_test shiny_sort_test sort_tomic sortInput sortServer tidy_to_triple tomic_sort_status tomic_to triple_to_tidy update_tidy_omic update_tomic

Dependencies:backports base64enc bit bit64 bslib cachem checkmate cli clipr colorspace commonmark cpp11 crayon digest dplyr fansi farver fastmap fontawesome fs generics ggplot2 glue gtable hms htmltools httpuv isoband jquerylib jsonlite labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme pillar pkgconfig plyr prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readr reshape2 rlang sass scales shiny sourcetools stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr xtable

R'Omic: high-dimensional data manipulation

Rendered fromromic.Rmdusingknitr::rmarkdownon Oct 15 2024.

Last update: 2023-02-02
Started: 2021-05-18

Help page	Topics
Add PCA Loadings	add_pcs
Flow	app_flow
Interactive Heatmap	app_heatmap
PC Plot	app_pcs
Brauer 2008	brauer_2008 brauer_2008_tidy brauer_2008_triple
Center T* Omic	center_tomic
Check Tidy Omic	check_tidy_omic
Check T*Omic	check_tomic
Check Triple Omic	check_triple_omic
Convert Wide to Tidy Omic	convert_wide_to_tidy_omic
Create Tidy Omic	create_tidy_omic
Create Triple Omic	create_triple_omic
Downsample Heatmap	downsample_heatmap
Export T*Omic in Tidy Format	export_tomic_as_tidy
Export T*Omic as Triple	export_tomic_as_triple
Export T*Omic as Wide Data	export_tomic_as_wide
Filter T* Omics	filter_tomic
Filter Input	filterInput
Filter Server	filterServer
Format Names for Plotting	format_names_for_plotting
Get Design Table	get_design_tbl
Get Tomic Table	get_tomic_table
ggBivariate Output	ggBivOutput
ggBivariate Server	ggBivServer
ggplot Output	ggplotOutput
ggplot Server	ggplotServer
ggUnivariate Output	ggUnivOutput
ggUnivariate Server	ggUnivServer
Hierarchical clustering order	hclust_order
Impute Missing Values	impute_missing_values
Infer Tomic Table Type	infer_tomic_table_type
Lasso Input	lassoInput
Lasso Server	lassoServer
Organize Input	organizeInput
Organize Servers	organizeServer
Bivariate Plot	plot_bivariate
Plot Heatmap	plot_heatmap
Univariate Plot	plot_univariate
Plot Saver Input	plotsaverInput
Plot Saver Server	plotsaverServer
Prepare Example Datasets	prepare_example_datasets
Reconcile Triple Omic	reconcile_triple_omic
Remove Missing Values	remove_missing_values
Shiny Filter Test	shiny_filter_test
Shiny ggBivariate Test	shiny_ggbiv_test
Shiny ggplot Test	shiny_ggplot_test
Shiny ggUnivariate Test	shiny_gguniv_test
Shiny Lasso Test	shiny_lasso_test
Shiny Lasso Test w/ Reactive Values	shiny_lasso_test_reactval
Shiny Organize Test	shiny_organize_test
Shiny Plot Saver Test	shiny_plotsaver_test
Shiny Sort Test	shiny_sort_test
Sort Triple Omic	sort_tomic
Sort Triple Arrange	sort_triple_arrange
Sort Triple Hclust	sort_triple_hclust
Sort Input	sortInput
Sort Server	sortServer
Tidy omic to triple omic	tidy_to_triple
T* Omic Sort Status	tomic_sort_status
T* Omic To	tomic_to
Triple Omic to Tidy Omic	triple_to_tidy
Try brushedPoints	try_brushedPoints
Update Tidy Omic	update_tidy_omic
Update T* Omic	update_tomic
Var Partial Match	var_partial_match

Package: romic 1.1.3

romic: R for High-Dimensional Omic Data

R'Omic: high-dimensional data manipulation

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