ReporterScore0.1.9 package

Generalized Reporter Score-Based Enrichment Analysis for Omics Data

c_means

Test the proper clusters k for c_means

combine_rs_res

Combine the results of 'step by step GRSA'

custom_modulelist_from_org

Custom modulelist from a specific organism

custom_modulelist

Build a custom modulelist

export_report_table

Export report score result tables

gene2ko

Transfer gene symbol table to KO table

get_features

get features in a modulelist

get_reporter_score

Calculate reporter score

GOlist

The GOlist used for enrichment.

KO_abundance

The KOs abundance table and group table.

KO_enrich

Perform enrichment analysis

KO_fisher

Perform fisher's exact enrichment analysis

KO_gsa

Perform gene set analysis

KO_gsea

Perform gene set enrichment analysis

KO_gsva

Perform Gene Set Variation Analysis

KO_padog

Perform Pathway Analysis with Down-weighting of Overlapping Genes (PAD...

KO_safe

Perform Significance Analysis of Function and Expression

KO_sea

Perform Simultaneous Enrichment Analysis

ko.test

Differential analysis or Correlation analysis for KO-abundance table

load_CARDinfo

Load the CARDinfo (from CARD database)

load_GOlist

Load the GOlist (from 'GO' database)

load_htable

Load the specific table (from 'KEGG')

modify_description

Modify the pathway description before plotting

pipe

Pipe operator

plot_enrich_res

Plot enrich_res

plot_features_box

Plot features boxplot

plot_features_distribution

plot the Z-score of features distribution

plot_features_heatmap

Plot features heatmap

plot_features_in_pathway

Plot features trend in one pathway or module

plot_features_network

Plot features network

plot_htable

Plot htable levels

plot_KEGG_map

plot_KEGG_map

plot_report_circle_packing

Plot the reporter_res as circle_packing

plot_report

Plot the reporter_res

plot_significance

Plot the significance of pathway

plot.cm_res

Plot c_means result

print.reporter_score

Print reporter_score

print.rs_by_cm

Print rs_by_cm

pvalue2zs

Transfer p-value of KOs to Z-score

reporter_score

One step to get the reporter score of your KO abundance table.

ReporterScore-package

ReporterScore: Generalized Reporter Score-Based Enrichment Analysis fo...

RSA_by_cm

Reporter score analysis after C-means clustering

up_level_KO

Upgrade the KO level

update_CARDinfo

update CARDinfo from (from 'CARD' database)

update_GOlist

Update the GO2gene files (from 'GO' database)

update_KEGG

Update files from 'KEGG'

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.

  • Maintainer: Chen Peng
  • License: GPL-3
  • Last published: 2024-11-28