Package: hipathia 3.5.0

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]

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

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

Peer review:

Datasets:
  • DAdata - Wilcoxon and limma comparison object for nodes, pathways and functional annotations
  • brca - BRCA gene expression dataset as SummarizedExperiment
  • brca_data - BRCA gene expression dataset
  • brca_design - BRCA experimental design
  • comp - Wilcoxon comparison of pathways object
  • 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-3.5.0(bioc 3.20)hipathia-3.4.0(bioc 3.19)

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

bioconductor-package

36 exports 1.00 score 150 dependencies

Last updated 2 months agofrom:8457cecffb

Exports:create_reportDAcompDAoverviewDAreportDAsummaryDAtopdefine_colorsdo_pcado_wilcoxonget_go_namesget_node_namesget_nodes_dataget_path_namesget_paths_dataget_pathways_annotationsget_pathways_listget_pathways_summaryheatmap_plothheadhipathiaload_pathwaysmgi_from_sifmultiple_pca_plotnode_colornode_color_per_denormalize_datanormalize_pathspaths_to_go_ancestorpathway_comparison_plotpca_plotplotVGquantify_termssave_resultstop_pathwaystranslate_datavisualize_report

Dependencies:abindAnnotationDbiAnnotationHubaskpassbackportsbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbootbroombslibcachemcarcarDataclicodetoolscoincolorspacecorrplotcowplotcpp11crayoncurlDBIdbplyrDelayedArrayDerivdigestdoBydplyrevaluatefansifarverfastmapfilelockfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelibcoinlifecyclelimmalme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoiseMetBrewermgcvmicrobenchmarkmimeminqamodelrmodeltoolsmultcompMultiAssayExperimentmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplogrplyrpngpolynompreprocessCorepromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownRSQLiterstatixS4ArraysS4VectorssandwichsassscalesservrSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsysTH.datatibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevisNetworkwithrxfunXVectoryamlzlibbioczoo

Readme and manuals

Help Manual

Help pageTopics
Annotates functions to pathwaysannotate_paths
BRCA gene expression dataset as SummarizedExperimentbrca
BRCA gene expression datasetbrca_data
BRCA experimental designbrca_design
Wilcoxon comparison of pathways objectcomp
Create visualization HTMLcreate_report
Compares the gene expression, pathway activation level and the function activation level of theDAcomp
Wilcoxon and limma comparison object for nodes, pathways and functional annotationsDAdata
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 HTMLDAreport
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 Analysisdo_pca
Apply Wilcoxon testdo_wilcoxon
Normalized BRCA gene expression datasetexp_data
Tranlates GO IDs to GO namesget_go_names
Get highest common GO ancestor of GO annotationsget_highest_sig_ancestor
Tranlates node IDs to node namesget_node_names
Gets the object of node activation valuesget_nodes_data
Tranlates path IDs to path namesget_path_names
Gets the object of subpathway activation valuesget_paths_data
Returns functions related to a pathwayget_pathway_functions
Get Pathways functional annotationsget_pathways_annotations
Lists the IDs of the pathways in a pathways objectget_pathways_list
Compute pathway summaryget_pathways_summary
Gene Ontology matrix of the BRCA gene expression datasetgo_vals
Plots subpathways heatmapheatmap_plot
Head function for SummarizedExperiment, data.frames and matrix objectshhead
Results objecthidata
Computes the level of activation of the subpathways for each of the sampleshipathia
Upgrade igraphs to current versionigraphs_upgrade
Checks whether a species is acceptedis_accepted_species
Loads annotations objectload_annofuns
Loads functional annotations to genesload_annots
Loads table of translation from HGNC to Entrezload_entrez_hgnc
Loads GO graph informationload_gobp_frame
Loads GO graphload_gobp_net
Loads object with graph informationload_mgi
Loads the pathways object.load_pathways
Loads object with pseudo graph informationload_pseudo_mgi
Loads table of referencesload_xref
Create a Pathways object from SIF filesmgi_from_sif
Plots multiple components of a PCAmultiple_pca_plot
Get colors of the nodes from a comparison filenode_color
Colors of the nodes by its differential expressionnode_color_per_de
Normalize expression data from a SummarizedExperiment or matrix to be used in 'hipathia'normalize_data
Normalize the pathway matrix by rowsnormalize_paths
Pathways matrix of the BRCA gene expression datasetpath_vals
Create path results table with highest significant GO ancestorspaths_to_go_ancestor
Plots pathway with colored significant pathspathway_comparison_plot
Pathways object including pathways has03320 and hsa04012.pathways
Plots two components of a PCApca_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 subpathwaysquantify_terms
Results objectresults
Save results to foldersave_results
Computes pathway significancetop_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 reportvisualize_report