Package: EGAD 1.41.0

Sara Ballouz

EGAD: Extending guilt by association by degree

The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.

Authors:Sara Ballouz [aut, cre], Melanie Weber [aut, ctb], Paul Pavlidis [aut], Jesse Gillis [aut, ctb]

EGAD_1.41.0.tar.gz
EGAD_1.41.0.zip(r-4.7)EGAD_1.41.0.zip(r-4.6)EGAD_1.41.0.zip(r-4.5)
EGAD_1.41.0.tgz(r-4.6-any)EGAD_1.41.0.tgz(r-4.5-any)
EGAD_1.41.0.tar.gz(r-4.7-any)EGAD_1.41.0.tar.gz(r-4.6-any)
EGAD_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
EGAD/json (API)
NEWS

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

On BioConductor:EGAD-1.41.0(bioc 3.24)EGAD-1.40.0(bioc 3.23)

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

softwarefunctionalgenomicssystemsbiologygenepredictionfunctionalpredictionnetworkenrichmentgraphandnetworknetwork

5.00 score 101 scripts 408 downloads 19 mentions 44 exports 80 dependencies

Last updated from:8d95fa7d7a. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR193
linux-devel-x86_64WARNING349
source / vignettesERROR287
linux-release-x86_64WARNING375
macos-release-arm64WARNING229
macos-oldrel-arm64WARNING225
windows-develWARNING302
windows-releaseWARNING247
windows-oldrelWARNING283
wasm-releaseOK140

Exports:assortativityauc_multifuncauprcauroc_analyticbuild_binary_networkbuild_coexp_expressionSetbuild_coexp_GEOIDbuild_coexp_networkbuild_semantic_similarity_networkbuild_weighted_networkcalculate_multifuncconv_smootherextend_networkfilter_networkfilter_network_colsfilter_network_rowsfilter_orthologsfmeasureget_aucget_biogridget_countsget_densityget_expression_data_gemmaget_expression_matrix_from_GEOget_phenocartaget_prcget_rocmake_annotationsmake_gene_networkmake_genelistmake_transparentneighbor_votingnode_degreeplot_densitiesplot_density_compareplot_distributionplot_network_heatmapplot_prcplot_rocplot_roc_overlayplot_value_comparepredictionsrepmatrun_GBA

Dependencies:abindaskpassBiobaseBiocGenericsbitbit64bitopscaToolsclicliprcpp11crayoncurldata.tableDelayedArraydplyrgenericsGenomicRangesGEOquerygluegplotsgtoolshmshttrhttr2igraphimputeIRangesjsonliteKernSmoothlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezrlangrvestS4ArraysS4VectorsselectrSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbutf8vctrsvroomwithrXMLxml2XVectorzoo

Readme and manuals

Help Manual

Help pageTopics
Calculating network assortativityassortativity
Human GENCODE annotations (v22)attr.human
Mouse GENCODE annotations (M7)attr.mouse
Calculating AUC for functional groups from ranked listsauc_multifunc
Area under the precision recall curveauprc
Area under the receiver operating characteristic curveauroc_analytic
BIOGRID v3.4.126biogrid
Builds a binary networkbuild_binary_network
Builds a coexpression network from an expressionSetbuild_coexp_expressionSet
Builds a coexpression network given a GEO IDbuild_coexp_GEOID
Builds a coexpression network from an expressionSetbuild_coexp_network
Builds a semantic similarity networkbuild_semantic_similarity_network
Builds a weighted networkbuild_weighted_network
Performing multifunctionality analysiscalculate_multifunc
Plot smoothed curveconv_smoother
Example of annotationsexample_annotations
Example of binary networkexample_binary_network
Example of binary networkexample_coexpression
Example of binary networkexample_neighbor_voting
Builds an extended network from a binary networkextend_network
Filter on matrixfilter_network
Filter on columnsfilter_network_cols
Filter on rowsfilter_network_rows
Filter on orthologsfilter_orthologs
Fmeasure of precision-recallfmeasure
Genes from BIOGRID v3.4.126genes
Calculates the area under a curveget_auc
Downloading and filtering BIOGRIDget_biogrid
Get countsget_counts
Get densityget_density
Obtain expression matrix from the GEMMA databaseget_expression_data_gemma
Obtain expression matrix from GEO databaseget_expression_matrix_from_GEO
Downloading and filtering Phenocartaget_phenocarta
Build precision-recall curveget_prc
Build receiver operating characteristic curveget_roc
GO - humanGO.human
GO - mouseGO.mouse
Gene ontology vocabularyGO.voc
Creating gene annotationsmake_annotations
Creating gene-by-gene networkmake_gene_network
Creating list of all genes in the data set.make_genelist
Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)make_transparent
Evaluating Gene Function Predictionneighbor_voting
Calculate node degreenode_degree
Gene orthologsortho
Phenocartapheno
Plot densitiesplot_densities
Plot density comparisonsplot_density_compare
Plot distribution histogramplot_distribution
Plot network heatmapplot_network_heatmap
Plot precision recall curveplot_prc
Plot receiver operating characteristic curveplot_roc
Plot ROC overlayplot_roc_overlay
Plot value comparisonsplot_value_compare
Performing Gene Function Predictionpredictions
Rep function for matricesrepmat
Performing 'Guilt by Association' Analysisrun_GBA