Package: romic 1.2.4

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]

romic_1.2.4.tar.gz
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romic_1.2.4.tgz(r-4.5-any)romic_1.2.4.tgz(r-4.4-any)romic_1.2.4.tgz(r-4.3-any)
romic_1.2.4.tar.gz(r-4.5-noble)romic_1.2.4.tar.gz(r-4.4-noble)
romic_1.2.4.tgz(r-4.4-emscripten)romic_1.2.4.tgz(r-4.3-emscripten)
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'))

Bug tracker:https://github.com/calico/romic/issues

Pkgdown site:https://calico.github.io

Datasets:

On CRAN:

Conda:

4.78 score 10 scripts 170 downloads 60 exports 72 dependencies

Last updated 6 months agofrom:791260b8c2. Checks:3 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 31 2025
R-4.5-winNOTEMar 31 2025
R-4.5-macNOTEMar 31 2025
R-4.5-linuxNOTEMar 31 2025
R-4.4-winNOTEMar 31 2025
R-4.4-macNOTEMar 31 2025
R-4.4-linuxNOTEMar 31 2025
R-4.3-winOKMar 31 2025
R-4.3-macOKMar 31 2025

Exports:add_pcsapp_flowapp_heatmapapp_pcscalculate_sample_mahalanobis_distancescenter_tomiccheck_designcheck_tomicconvert_wide_to_tidy_omiccreate_tidy_omiccreate_triple_omicexport_tomic_as_tidyexport_tomic_as_tripleexport_tomic_as_widefilter_tomicfilterInputfilterServerformat_names_for_plottingget_design_tblget_tomic_tableggBivOutputggBivServerggplotOutputggplotServerggUnivOutputggUnivServerhclust_orderimpute_missing_valueslassoInputlassoServerorganizeInputorganizeServerplot_bivariateplot_heatmapplot_missing_valuesplot_univariateplotsaverInputplotsaverServerreform_tidy_omicremove_missing_valuesshiny_filter_testshiny_ggbiv_testshiny_ggplot_testshiny_gguniv_testshiny_lasso_testshiny_lasso_test_reactvalshiny_organize_testshiny_plotsaver_testshiny_sort_testsort_tomicsortInputsortServertidy_to_tripletomic_sort_statustomic_totomic_to_matrixtriple_to_tidyupdate_sample_factorsupdate_tidy_omicupdate_tomic

Dependencies:backportsbase64encbitbit64bslibcachemcheckmateclicliprcolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgenericsggplot2gluegtablehmshtmltoolshttpuvisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigplyrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrreshape2rlangsassscalesshinysourcetoolsstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxtable

R'Omic: high-dimensional data manipulation

Rendered fromromic.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2023-01-18
Started: 2021-05-14

Readme and manuals

Help Manual

Help pageTopics
Add PCA Loadingsadd_pcs
Flowapp_flow
Interactive Heatmapapp_heatmap
PC Plotapp_pcs
Brauer 2008brauer_2008 brauer_2008_tidy brauer_2008_triple
Calculate Sample Mahalanobis Distancescalculate_sample_mahalanobis_distances
Center T* Omiccenter_tomic
Check Designcheck_design
Check Tidy Omiccheck_tidy_omic
Check T*Omiccheck_tomic
Check Triple Omiccheck_triple_omic
Convert Wide to Tidy Omicconvert_wide_to_tidy_omic
Create Tidy Omiccreate_tidy_omic
Create Triple Omiccreate_triple_omic
Downsample Heatmapdownsample_heatmap
Export T*Omic in Tidy Formatexport_tomic_as_tidy
Export T*Omic as Tripleexport_tomic_as_triple
Export T*Omic as Wide Dataexport_tomic_as_wide
Filter T* Omicsfilter_tomic
Filter InputfilterInput
Filter ServerfilterServer
Format Names for Plottingformat_names_for_plotting
Get Design Tableget_design_tbl
Get Tomic Tableget_tomic_table
ggBivariate OutputggBivOutput
ggBivariate ServerggBivServer
ggplot OutputggplotOutput
ggplot ServerggplotServer
ggUnivariate OutputggUnivOutput
ggUnivariate ServerggUnivServer
Hierarchical clustering orderhclust_order
Impute Missing Valuesimpute_missing_values
Infer Tomic Table Typeinfer_tomic_table_type
Lasso InputlassoInput
Lasso ServerlassoServer
Organize InputorganizeInput
Organize ServersorganizeServer
Bivariate Plotplot_bivariate
Plot Heatmapplot_heatmap
Plot Missing Valuesplot_missing_values
Univariate Plotplot_univariate
Plot Saver InputplotsaverInput
Plot Saver ServerplotsaverServer
Prepare Example Datasetsprepare_example_datasets
Reconcile Triple Omicreconcile_triple_omic
Reform Tidy Omicreform_tidy_omic
Remove Missing Valuesremove_missing_values
Shiny Filter Testshiny_filter_test
Shiny ggBivariate Testshiny_ggbiv_test
Shiny ggplot Testshiny_ggplot_test
Shiny ggUnivariate Testshiny_gguniv_test
Shiny Lasso Testshiny_lasso_test
Shiny Lasso Test w/ Reactive Valuesshiny_lasso_test_reactval
Shiny Organize Testshiny_organize_test
Shiny Plot Saver Testshiny_plotsaver_test
Shiny Sort Testshiny_sort_test
Sort Triple Omicsort_tomic
Sort Triple Arrangesort_triple_arrange
Sort Triple Hclustsort_triple_hclust
Sort InputsortInput
Sort ServersortServer
Tidy omic to triple omictidy_to_triple
T* Omic Sort Statustomic_sort_status
T* Omic Totomic_to
Tomic To Matrixtomic_to_matrix
Triple Omic to Tidy Omictriple_to_tidy
Try brushedPointstry_brushedPoints
Update Sample Factorsupdate_sample_factors
Update Tidy Omicupdate_tidy_omic
Update T* Omicupdate_tomic
Var Partial Matchvar_partial_match