Package: ReporterScore 0.2.6

Chen Peng

ReporterScore: Generalized Reporter Score-Based Enrichment Analysis for Omics Data

Inspired by the classic 'RSA', we developed the improved 'Generalized Reporter Score-based Analysis (GRSA)' method, implemented in the R package 'ReporterScore', along with comprehensive visualization methods and pathway databases. 'GRSA' is a threshold-free method that works well with all types of biomedical features, such as genes, chemical compounds, and microbial species. Importantly, the 'GRSA' supports multi-group and longitudinal experimental designs, because of the included multi-group-compatible statistical methods.

Authors:Chen Peng [aut, cre]

ReporterScore_0.2.6.tar.gz
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ReporterScore_0.2.6.tgz(r-4.6-any)ReporterScore_0.2.6.tgz(r-4.5-any)
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ReporterScore_0.2.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ReporterScore/json (API)

# Install 'ReporterScore' in R:

install.packages('ReporterScore', repos = c('https://asa12138.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/asa12138/reporterscore/issues

Datasets:

Compound_htable - Compound htable from 'KEGG'
CPDlist - The CPDlist used for enrichment.
genedf - Human gene table
hsa_kegg_pathway - Pathway information for "hsa"
KO_abundance - The KOs abundance table and group table.
KO_htable - KO htable from 'KEGG'
KOlist - The KOlist used for enrichment.
metadata - The KOs abundance table and group table.
mmu_kegg_pathway - Pathway information for "mmu"
Module_htable - Module htable from 'KEGG'
Pathway_htable - Pathway htable from 'KEGG'
reporter_score_res - 'reporter_score()' result from KO_abundance_test
reporter_score_res2 - 'reporter_score()' result from KO_abundance_test

On CRAN:

6.29 score 88 stars 22 scripts 416 downloads 82 exports 38 dependencies

Last updated from:8df9e8cbd6. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	327
source / vignettes	OK	365
linux-release-x86_64	OK	362
macos-release-arm64	OK	125
macos-oldrel-arm64	OK	211
windows-devel	OK	195
windows-release	OK	272
windows-oldrel	OK	264
wasm-release	OK	288

Exports:%>%as.enrich_res c_means c_net_from_pathway_xml cm_test_k combine_rs_res custom_modulelist custom_modulelist_from_org download_org_pathway export_report_table extract_cluster gene2ko get_all_pathway_net_index get_features get_KOs get_org_pathway get_reporter_score GRSA GRSA_by_cm KO_enrich KO_fisher KO_gsa KO_gsea KO_gsva KO_padog KO_safe KO_sea ko.test load_CARDinfo load_CAZy_info load_Compound_htable load_CPDlist load_Enzyme_htable load_Enzyme_info load_GOinfo load_GOlist load_htable load_KO_desc load_KO_htable load_KOlist load_Module_htable load_org_pathway load_Pathway_htable load_pathway_xml_ls modify_description pathway_net_index plot_c_means plot_enrich_res plot_features_box plot_features_distribution plot_features_heatmap plot_features_in_pathway plot_features_network plot_htable plot_KEGG_map plot_KOs_box plot_KOs_distribution plot_KOs_heatmap plot_KOs_in_pathway plot_KOs_network plot_pathway_net plot_report plot_report_bar plot_report_circle_packing plot_significance pvalue2zs reporter_score RSA RSA_by_cm RSA_by_mg transform_modulelist up_level_KO update_CARDinfo update_CAZy_info update_Enzyme_info update_GOinfo update_GOlist update_htable update_KEGG update_KO_file update_org_pathway update_pathway_xml_ls

Dependencies:cli codetools cpp11 dplyr farver foreach generics ggnewscale ggplot2 ggrepel glue gtable isoband iterators labeling lifecycle magrittr pcutils pillar pkgconfig plyr purrr R6 RColorBrewer Rcpp reshape2 rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

ReporterScore

Rendered fromReporterScore.Rmdusingknitr::rmarkdown

Last update: 2024-03-20
Started: 2023-06-21

Help page	Topics
Create a network from KEGG pathway XML files	c_net_from_pathway_xml
Test the proper clusters k for c_means	cm_test_k c_means
Combine the results of 'step by step GRSA'	combine_rs_res
Compound htable from 'KEGG'	Compound_htable
The CPDlist used for enrichment.	CPDlist
Build a custom modulelist	custom_modulelist transform_modulelist
Custom modulelist from a specific organism	custom_modulelist_from_org
Export report score result tables	export_report_table
Transfer gene symbol table to KO table	gene2ko
human gene table	genedf
Create an index for all KEGG pathway networks	get_all_pathway_net_index
get features in a modulelist	get_features get_KOs
Calculate reporter score	get_reporter_score
The GOlist used for enrichment.	GOlist
pathway information for "hsa"	hsa_kegg_pathway
The KOs abundance table and group table.	KO_abundance metadata
Perform enrichment analysis	as.enrich_res KO_enrich
Perform fisher's exact enrichment analysis	KO_fisher
Perform gene set analysis	KO_gsa
Perform gene set enrichment analysis	KO_gsea
Perform Gene Set Variation Analysis	KO_gsva
KO htable from 'KEGG'	KO_htable
Perform Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)	KO_padog
Perform Significance Analysis of Function and Expression	KO_safe
Perform Simultaneous Enrichment Analysis	KO_sea
Differential analysis or Correlation analysis for KO-abundance table	ko.test
The KOlist used for enrichment.	KOlist
Load the CARDinfo (from CARD database)	load_CARDinfo
Load the CAZy_info (from CAZy database)	load_CAZy_info
Load the Enzyme_info (from ExPASy Enzyme database)	load_Enzyme_info
Load the GOlist (from 'GO' database)	load_GOinfo load_GOlist
Load the specific table (from 'KEGG')	load_Compound_htable load_CPDlist load_Enzyme_htable load_htable load_KOlist load_KO_desc load_KO_htable load_Module_htable load_org_pathway load_Pathway_htable
Load KEGG pathway XML file list	load_pathway_xml_ls
pathway information for "mmu"	mmu_kegg_pathway
Modify the pathway description before plotting	modify_description
Module htable from 'KEGG'	Module_htable
Parse enzyme.dat file into a structured data frame	parse_enzyme_dat
Pathway htable from 'KEGG'	Pathway_htable
Create a pathway network index data.frame	pathway_net_index
Plot enrich_res	plot.enrich_res plot_enrich_res
Plot features boxplot	plot_features_box plot_KOs_box
plot the Z-score of features distribution	plot_features_distribution plot_KOs_distribution
Plot features heatmap	plot_features_heatmap plot_KOs_heatmap
Plot features trend in one pathway or module	plot_features_in_pathway plot_KOs_in_pathway
Plot features network	plot_features_network plot_KOs_network
Plot htable levels	plot_htable
plot_KEGG_map	plot_KEGG_map
Plot a KEGG pathway network	plot_pathway_net
Plot the reporter_res	plot_report plot_report_bar
Plot the reporter_res as circle_packing	plot_report_circle_packing
Plot the significance of pathway	plot_significance
Plot c_means result	plot.cm_res
Print reporter_score	print.reporter_score
Print rs_by_cm	print.rs_by_cm
Print rs_by_mg	print.rs_by_mg
Transfer p-value of KOs to Z-score	pvalue2zs
One step to get the reporter score of your KO abundance table.	GRSA reporter_score RSA
`reporter_score()` result from KO_abundance_test	reporter_score_res reporter_score_res2
Reporter score analysis after C-means clustering	extract_cluster GRSA_by_cm plot_c_means RSA_by_cm
Reporter score analysis by pairwise comparison in multi-group	RSA_by_mg
Upgrade the KO level	up_level_KO
update CARDinfo from (from 'CARD' database)	update_CARDinfo
Update CAZy_info from CAZy database	update_CAZy_info
Update Enzyme_info from ExPASy Enzyme database	update_Enzyme_info
Update the GO2gene files (from 'GO' database)	update_GOinfo update_GOlist
Update files from 'KEGG'	download_org_pathway get_org_pathway update_htable update_KEGG update_KO_file update_org_pathway
Download KEGG pathway XML files and create networks	update_pathway_xml_ls

Package: ReporterScore 0.2.6

ReporterScore: Generalized Reporter Score-Based Enrichment Analysis for Omics Data

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