Package: GeneSCARAB 0.99.3

Marcos Ramos-González

GeneSCARAB: Gene Set Circular Analysis for Rhythms Ascertainment in Bioprocesses

GeneSCARAB includes a range of features designed to enable a robust and comprehensive analysis of the circular distributions of biomolecules (genes, proteins, metabolites, ...) associated with bioprocesses in any species. It is specifically designed for circadian omics studies and facilitates data organization, statistical analysis, and the visualization of results. It works with the output of standard rhythm detection software, such as CircaCompare, MetaCycle or RAIN.

Authors:Marcos Ramos-González [aut, cre], Emma Serrano-Pérez [ctb], Víctor Ramos-González [ctb], Mercedes García-González [ctb], Francisco J. Romero-Campero [ctb]

GeneSCARAB_0.99.3.tar.gz
GeneSCARAB_0.99.3.zip(r-4.7-any)GeneSCARAB_0.99.3.zip(r-4.6-any)GeneSCARAB_0.99.3.zip(r-4.5-any)
GeneSCARAB_0.99.3.tgz(r-4.6-any)GeneSCARAB_0.99.3.tgz(r-4.5-any)
GeneSCARAB_0.99.3.tar.gz(r-4.7-any)GeneSCARAB_0.99.3.tar.gz(r-4.6-any)
GeneSCARAB_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GeneSCARAB/json (API)

# Install 'GeneSCARAB' in R:

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

Bug tracker:https://github.com/ramosgonzmarc/genescarab/issues

Datasets:

circa_table_genescarab - Circa_table_genescarab

On CRAN:

genetics multiplecomparison proteomics software systemsbiology timecourse transcriptomics statisticalmethod

3.65 score 13 exports 134 dependencies

Last updated from:ea64178b43. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	215
linux-devel	OK	318
source / vignettes	OK	311
linux-release	OK	325
macos-release	OK	236
macos-oldrel	OK	164
windows-devel	OK	238
windows-release	OK	247
windows-oldrel	OK	233
wasm-release	OK	216

Exports:circular_boxplot circular_dotplot circular_histogram complete_circular_table complete_circular_table_grouped create_gene_list_go create_gene_list_kegg gene_contribution_to_set gene_list_to_phases load_example_annot multimodal_analysis test_against_gen_dist test_two_dist

Dependencies:AnnotationDbi askpass base64enc BH bigassertr bigparallelr bigstatsr Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 blob boot bslib cachem circlize CircMLE circular Ckmeans.1d.dp class classInt cli clue cluster codetools colorspace ComplexHeatmap cowplot cpp11 crayon curl DBI digest Directional doParallel e1071 energy evaluate farver fastmap ff flock fontawesome foreach fs generics GetoptLong ggplot2 GlobalOptions glue GO.db gsl gtable highr htmltools htmlwidgets httr IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lattice lifecycle magrittr Matrix matrixStats memoise MetBrewer mime mvtnorm openssl OptCirClust parallelly pillar pkgconfig plotrix plyr png proxy ps R6 rangen rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack reshape2 Rfast Rfast2 rgl RhpcBLASctl rjson rlang rmarkdown rmio Rnanoflann rnaturalearth RSpectra RSQLite s2 S4Vectors S7 sass scales Seqinfo sf shape stringi stringr sys terra tibble tinytex units utf8 vctrs viridisLite withr wk xfun XVector yaml zigg

GeneSCARAB

Rendered fromGeneSCARAB.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-07-27

Help page	Topics
Creation of the circular table and deviation from the uniform distribution for a single set	.create_circular_table
Creation of the circular table and deviation from the uniform distribution for a single set of grouped data	.create_circular_table_grouped
Extraction of all ancestors of a given GO terms vector	.get_ancestor_for_gene_lists
Helper circular grid creation	.helper_init_plot
HR test's p-value calculation for grouped data	.HermansRasson2PGroupedRad
Critical value calculation for HR test	.HermansRasson2T
Input checking for complete_circular_table and complete_circular_table_grouped	.input_complete_circular_table
Input checking for .create_circular_table and .create_circular_table_grouped	.input_create_circular_table
Input checking for create_gene_list_go	.input_create_gene_list_go
Input checking for create_gene_list_kegg	.input_create_gene_list_kegg
Input checking for gene_contribution_to_set	.input_gene_contribution
Kuiper test's p-value calculation for grouped data	.KuiperPGroupedRad
Helper legend builder for dotplot and histogram	.legend_builder
Helper legend builder for boxplot	.legend_builder_boxplot
Identification of different modes	.multimodal_modes_test
Extraction of KEGG pathways from KO terms	.pathways_from_kos
Rao's spacing test's p-value calculation for grouped data	.RaoPGroupedRad
Rao's spacing test's p-value calculation for ungrouped data	.RaoTestUngroupedRad
Critical value calculation for Rao's spacing test	.RaoTestValue
Helper function to construct table from circular data	.table_builder
Helper track creation boxplot for box cutting the origin	.track_box_box_cut
Helper track creation boxplot without cut	.track_box_no_cut
Helper track creation boxplot for segments cutting the origin	.track_box_segments_cut
Helper track creation dotplot	.track_dot
circa_table_genescarab	circa_table_genescarab
Circular boxplot	circular_boxplot
Circular dotplot	circular_dotplot
Circular histogram	circular_histogram
Creation of the circular table and deviation from the uniform distribution for a phases list	complete_circular_table
Creation of the circular table and deviation from the uniform distribution for a discrete (grouped) phases list	complete_circular_table_grouped
Creation of input lists for GO terms from an annotation package	create_gene_list_go
Creation of input lists for KEGG pathways from an annotation package	create_gene_list_kegg
Contribution of each gene in a set to the temporal cohesion of the whole set	gene_contribution_to_set
Creation of phase table lists	gene_list_to_phases
GeneSCARAB: Gene Set Circular Analysis and Rhythms Ascertainment in Bioprocesses	GeneSCARAB-package GeneSCARAB
Loading annotation for examples and vignettes	load_example_annot
Multimodality analysis	multimodal_analysis
Deviation from the total experimental distribution for a phases list	test_against_gen_dist
Comparison of circular distributions between two conditions	test_two_dist

Package: GeneSCARAB 0.99.3

GeneSCARAB: Gene Set Circular Analysis for Rhythms Ascertainment in Bioprocesses

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