Package: hipathia 3.13.0

Marta R. Hidalgo

hipathia: HiPathia: High-throughput Pathway Analysis

Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway.

Authors:Marta R. Hidalgo [aut, cre], José Carbonell-Caballero [ctb], Francisco Salavert [ctb], Alicia Amadoz [ctb], Çankut Cubuk [ctb], Joaquin Dopazo [ctb]

hipathia_3.13.0.tar.gz
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hipathia_3.13.0.tgz(r-4.6-any)hipathia_3.13.0.tgz(r-4.5-any)
hipathia_3.13.0.tar.gz(r-4.7-any)hipathia_3.13.0.tar.gz(r-4.6-any)
hipathia_3.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hipathia/json (API)

# Install 'hipathia' in R:

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

Datasets:

brca - BRCA gene expression dataset as SummarizedExperiment
brca_data - BRCA gene expression dataset
brca_design - BRCA experimental design
comp - Wilcoxon comparison of pathways object
DAdata - Wilcoxon and limma comparison object for nodes, pathways and functional annotations
exp_data - Normalized BRCA gene expression dataset
go_vals - Gene Ontology matrix of the BRCA gene expression dataset
hidata - Results object
path_vals - Pathways matrix of the BRCA gene expression dataset
pathways - Pathways object including pathways has03320 and hsa04012.
results - Results object

On BioConductor:hipathia-3.13.0(bioc 3.24)hipathia-3.12.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

pathways graphandnetwork geneexpression genesignaling go

5.08 score 60 scripts 36 exports 145 dependencies

Last updated from:88814b548e. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	214
linux-devel-x86_64	NOTE	571
source / vignettes	OK	476
linux-release-x86_64	NOTE	594
macos-release-arm64	NOTE	392
macos-oldrel-arm64	NOTE	384
windows-devel	NOTE	462
windows-release	NOTE	450
windows-oldrel	NOTE	465
wasm-release	OK	166

Exports:create_report DAcomp DAoverview DAreport DAsummary DAtop define_colors do_pca do_wilcoxon get_go_names get_node_names get_nodes_data get_path_names get_paths_data get_pathways_annotations get_pathways_list get_pathways_summary heatmap_plot hhead hipathia load_pathways mgi_from_sif multiple_pca_plot node_color node_color_per_de normalize_data normalize_paths paths_to_go_ancestor pathway_comparison_plot pca_plot plotVG quantify_terms save_results top_pathways translate_data visualize_report

Dependencies:abind askpass backports base64enc Biobase BiocBaseUtils BiocGenerics boot broom bslib cachem car carData cli codetools coin colorspace corrplot cowplot cpp11 curl DelayedArray Deriv digest doBy dplyr evaluate farver fastmap filelock fontawesome forecast Formula fracdiff fs generics GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable highr htmltools htmlwidgets httpuv httr igraph IRanges isoband jquerylib jsonlite keyring knitr labeling later lattice libcoin lifecycle limma lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise MetBrewer mgcv microbenchmark mime minqa modelr modeltools multcomp MultiAssayExperiment mvtnorm nlme nloptr nnet numDeriv openssl otel pbkrtest pillar pkgconfig plyr polynom preprocessCore promises purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang rmarkdown rstatix S4Arrays S4Vectors S7 sandwich sass scales Seqinfo servr SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys TH.data tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viridisLite visNetwork withr xfun XML xml2 XVector yaml zen4R zoo

Hipathia Package

Rendered fromhipathia-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-03-20
Started: 2017-11-27

Help page	Topics
Annotates functions to pathways	annotate_paths
BRCA gene expression dataset as SummarizedExperiment	brca
BRCA gene expression dataset	brca_data
BRCA experimental design	brca_design
Wilcoxon comparison of pathways object	comp
Create visualization HTML	create_report
Compares the gene expression, pathway activation level and the function activation level of the	DAcomp
Wilcoxon and limma comparison object for nodes, pathways and functional annotations	DAdata
Table and plot of total number of altered and not altered nodes, paths and functions (Uniprot keywords and/or GO terms, if present).	DAoverview
Create visualization HTML	DAreport
Lists and plots the top 'n' altered pathways, taking into account the number of altered .	DAsummary
Lists and plots the top 'n' altered nodes, paths and functions (Uniprot keywords and/or GO terms, if present).	DAtop
Color palettes to be used in plots.	define_colors
Performs a Principal Components Analysis	do_pca
Apply Wilcoxon test	do_wilcoxon
Normalized BRCA gene expression dataset	exp_data
Loads a RData object and downloads it from Zenodo if necessary	get_file
Tranlates GO IDs to GO names	get_go_names
Get highest common GO ancestor of GO annotations	get_highest_sig_ancestor
Tranlates node IDs to node names	get_node_names
Gets the object of node activation values	get_nodes_data
Tranlates path IDs to path names	get_path_names
Gets the object of subpathway activation values	get_paths_data
Returns functions related to a pathway	get_pathway_functions
Get Pathways functional annotations	get_pathways_annotations
Lists the IDs of the pathways in a pathways object	get_pathways_list
Compute pathway summary	get_pathways_summary
Gene Ontology matrix of the BRCA gene expression dataset	go_vals
Plots subpathways heatmap	heatmap_plot
Head function for SummarizedExperiment, data.frames and matrix objects	hhead
Results object	hidata
Computes the level of activation of the subpathways for each of the samples	hipathia
Upgrade igraphs to current version	igraphs_upgrade
Checks whether a species is accepted	is_accepted_species
Loads annotations object	load_annofuns
Loads functional annotations to genes	load_annots
Loads table of translation from HGNC to Entrez	load_entrez_hgnc
Loads GO graph information	load_gobp_frame
Loads GO graph	load_gobp_net
Loads object with graph information	load_mgi
Loads the pathways object.	load_pathways
Loads object with pseudo graph information	load_pseudo_mgi
Loads table of references	load_xref
Create a Pathways object from SIF files	mgi_from_sif
Plots multiple components of a PCA	multiple_pca_plot
Get colors of the nodes from a comparison file	node_color
Colors of the nodes by its differential expression	node_color_per_de
Normalize expression data from a SummarizedExperiment or matrix to be used in 'hipathia'	normalize_data
Normalize the pathway matrix by rows	normalize_paths
Pathways matrix of the BRCA gene expression dataset	path_vals
Create path results table with highest significant GO ancestors	paths_to_go_ancestor
Plots pathway with colored significant paths	pathway_comparison_plot
Pathways object including pathways has03320 and hsa04012.	pathways
Plots two components of a PCA	pca_plot
Plots a pathway with or without the comparison information, using the visNetwork library.	plotVG
Computes the level of activation of the functions related to the previously computed subpathways	quantify_terms
Results object	results
Save results to folder	save_results
Computes pathway significance	top_pathways
Translation of the rownames IDs of a SummarizedExperiment to Entrez IDs.	translate_data
Translation of the rownames IDs of a matrix to Entrez IDs.	translate_matrix
Visualize a HiPathia report	visualize_report

Package: hipathia 3.13.0

hipathia: HiPathia: High-throughput Pathway Analysis

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