Package: ReporterScore 0.1.8

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]

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

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

Peer review:

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

Datasets:

On CRAN:

6.80 score 49 stars 13 scripts 247 downloads 70 exports 45 dependencies

Last updated 2 months agofrom:8e497d65dd. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winERROROct 29 2024
R-4.5-linuxERROROct 29 2024
R-4.4-winERROROct 29 2024
R-4.4-macERROROct 29 2024
R-4.3-winERROROct 29 2024
R-4.3-macERROROct 29 2024

Exports:%>%as.enrich_resc_meanscm_test_kcombine_rs_rescustom_modulelistcustom_modulelist_from_orgdownload_org_pathwayexport_report_tableextract_clustergene2koget_featuresget_KOsget_org_pathwayget_reporter_scoreGRSAGRSA_by_cmKO_enrichKO_fisherKO_gsaKO_gseaKO_gsvaKO_padogKO_safeKO_seako.testload_CARDinfoload_Compound_htableload_CPDlistload_GOinfoload_GOlistload_htableload_KO_descload_KO_htableload_KOlistload_Module_htableload_org_pathwayload_Pathway_htablemodify_descriptionplot_c_meansplot_enrich_resplot_features_boxplot_features_distributionplot_features_heatmapplot_features_in_pathwayplot_features_networkplot_htableplot_KEGG_mapplot_KOs_boxplot_KOs_distributionplot_KOs_heatmapplot_KOs_in_pathwayplot_KOs_networkplot_reportplot_report_barplot_report_circle_packingplot_significancepvalue2zsreporter_scoreRSARSA_by_cmtransform_modulelistup_level_KOupdate_CARDinfoupdate_GOinfoupdate_GOlistupdate_htableupdate_KEGGupdate_KO_fileupdate_org_pathway

Dependencies:clicodetoolscolorspacecpp11dplyrfansifarverforeachgenericsggnewscaleggplot2ggrepelgluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepcutilspillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

ReporterScore

Rendered fromReporterScore.Rmdusingknitr::rmarkdownon Oct 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Test the proper clusters k for c_meanscm_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 modulelistcustom_modulelist transform_modulelist
Custom modulelist from a specific organismcustom_modulelist_from_org
Export report score result tablesexport_report_table
Transfer gene symbol table to KO tablegene2ko
human gene tablegenedf
get features in a modulelistget_features get_KOs
Calculate reporter scoreget_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 analysisas.enrich_res KO_enrich
Perform fisher's exact enrichment analysisKO_fisher
Perform gene set analysisKO_gsa
Perform gene set enrichment analysisKO_gsea
Perform Gene Set Variation AnalysisKO_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 ExpressionKO_safe
Perform Simultaneous Enrichment AnalysisKO_sea
Differential analysis or Correlation analysis for KO-abundance tableko.test
The KOlist used for enrichment.KOlist
Load the CARDinfo (from CARD database)load_CARDinfo
Load the GOlist (from 'GO' database)load_GOinfo load_GOlist
Load the specific table (from 'KEGG')load_Compound_htable load_CPDlist load_htable load_KOlist load_KO_desc load_KO_htable load_Module_htable load_org_pathway load_Pathway_htable
pathway information for "mmu"mmu_kegg_pathway
Modify the pathway description before plottingmodify_description
Module htable from 'KEGG'Module_htable
Pathway htable from 'KEGG'Pathway_htable
Plot enrich_resplot.enrich_res plot_enrich_res
Plot features boxplotplot_features_box plot_KOs_box
plot the Z-score of features distributionplot_features_distribution plot_KOs_distribution
Plot features heatmapplot_features_heatmap plot_KOs_heatmap
Plot features trend in one pathway or moduleplot_features_in_pathway plot_KOs_in_pathway
Plot features networkplot_features_network plot_KOs_network
Plot htable levelsplot_htable
plot_KEGG_mapplot_KEGG_map
Plot the reporter_resplot_report plot_report_bar
Plot the reporter_res as circle_packingplot_report_circle_packing
Plot the significance of pathwayplot_significance
Plot c_means resultplot.cm_res
Print reporter_scoreprint.reporter_score
Print rs_by_cmprint.rs_by_cm
Transfer p-value of KOs to Z-scorepvalue2zs
One step to get the reporter score of your KO abundance table.GRSA reporter_score RSA
`reporter_score()` result from KO_abundance_testreporter_score_res reporter_score_res2
Reporter score analysis after C-means clusteringextract_cluster GRSA_by_cm plot_c_means RSA_by_cm
Upgrade the KO levelup_level_KO
update CARDinfo from (from 'CARD' database)update_CARDinfo
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