Package: EGAD 1.35.0

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_1.35.0.tar.gz
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EGAD.pdf |EGAD.html✨
EGAD/json (API)
NEWS

# Install 'EGAD' in R:

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

Datasets:

GO.human - GO - human
GO.mouse - GO - mouse
GO.voc - Gene ontology vocabulary
attr.human - Human GENCODE annotations
attr.mouse - Mouse GENCODE annotations
biogrid - BIOGRID v3.4.126
example_annotations - Example of annotations
example_binary_network - Example of binary network
example_coexpression - Example of binary network
example_neighbor_voting - Example of binary network
genes - Genes from BIOGRID v3.4.126
ortho - Gene orthologs
pheno - Phenocarta

On BioConductor:EGAD-1.33.0(bioc 3.20)EGAD-1.32.0(bioc 3.19)

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

software functionalgenomics systemsbiology geneprediction functionalprediction networkenrichment graphandnetwork network

3.92 score 83 scripts 206 downloads 44 exports 84 dependencies

Last updated 23 days agofrom:65e168f4b4. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	WARNING	Oct 30 2024
R-4.5-linux	WARNING	Oct 30 2024
R-4.4-win	WARNING	Oct 30 2024
R-4.4-mac	WARNING	Oct 30 2024
R-4.3-win	WARNING	Oct 30 2024
R-4.3-mac	WARNING	Oct 30 2024

Exports:assortativity auc_multifunc auprc auroc_analytic build_binary_network build_coexp_expressionSet build_coexp_GEOID build_coexp_network build_semantic_similarity_network build_weighted_network calculate_multifunc conv_smoother extend_network filter_network filter_network_cols filter_network_rows filter_orthologs fmeasure get_auc get_biogrid get_counts get_density get_expression_data_gemma get_expression_matrix_from_GEO get_phenocarta get_prc get_roc make_annotations make_gene_network make_genelist make_transparent neighbor_voting node_degree plot_densities plot_density_compare plot_distribution plot_network_heatmap plot_prc plot_roc plot_roc_overlay plot_value_compare predictions repmat run_GBA

Dependencies:abind askpass Biobase BiocGenerics bit bit64 bitops caTools cli clipr cpp11 crayon curl data.table DelayedArray dplyr fansi generics GenomeInfoDb GenomeInfoDbData GenomicRanges GEOquery glue gplots gtools hms httr httr2 igraph impute IRanges jsonlite KernSmooth lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig plyr prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez rlang rvest S4Arrays S4Vectors selectr SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XML xml2 XVector zlibbioc zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculating network assortativity	assortativity
Human GENCODE annotations (v22)	attr.human
Mouse GENCODE annotations (M7)	attr.mouse
Calculating AUC for functional groups from ranked lists	auc_multifunc
Area under the precision recall curve	auprc
Area under the receiver operating characteristic curve	auroc_analytic
BIOGRID v3.4.126	biogrid
Builds a binary network	build_binary_network
Builds a coexpression network from an expressionSet	build_coexp_expressionSet
Builds a coexpression network given a GEO ID	build_coexp_GEOID
Builds a coexpression network from an expressionSet	build_coexp_network
Builds a semantic similarity network	build_semantic_similarity_network
Builds a weighted network	build_weighted_network
Performing multifunctionality analysis	calculate_multifunc
Plot smoothed curve	conv_smoother
Example of annotations	example_annotations
Example of binary network	example_binary_network
Example of binary network	example_coexpression
Example of binary network	example_neighbor_voting
Builds an extended network from a binary network	extend_network
Filter on matrix	filter_network
Filter on columns	filter_network_cols
Filter on rows	filter_network_rows
Filter on orthologs	filter_orthologs
Fmeasure of precision-recall	fmeasure
Genes from BIOGRID v3.4.126	genes
Calculates the area under a curve	get_auc
Downloading and filtering BIOGRID	get_biogrid
Get counts	get_counts
Get density	get_density
Obtain expression matrix from the GEMMA database	get_expression_data_gemma
Obtain expression matrix from GEO database	get_expression_matrix_from_GEO
Downloading and filtering Phenocarta	get_phenocarta
Build precision-recall curve	get_prc
Build receiver operating characteristic curve	get_roc
GO - human	GO.human
GO - mouse	GO.mouse
Gene ontology vocabulary	GO.voc
Creating gene annotations	make_annotations
Creating gene-by-gene network	make_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 Prediction	neighbor_voting
Calculate node degree	node_degree
Gene orthologs	ortho
Phenocarta	pheno
Plot densities	plot_densities
Plot density comparisons	plot_density_compare
Plot distribution histogram	plot_distribution
Plot network heatmap	plot_network_heatmap
Plot precision recall curve	plot_prc
Plot receiver operating characteristic curve	plot_roc
Plot ROC overlay	plot_roc_overlay
Plot value comparisons	plot_value_compare
Performing Gene Function Prediction	predictions
Rep function for matrices	repmat
Performing 'Guilt by Association' Analysis	run_GBA