Package: BioCor 1.31.0

Lluís Revilla Sancho

BioCor: Functional similarities

Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships...

Authors:Lluís Revilla Sancho [aut, cre], Pau Sancho-Bru [ths], Juan José Salvatella Lozano [ths]

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NEWS

# Install 'BioCor' in R:

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

Bug tracker:https://github.com/llrs/biocor/issues

Pkgdown site:https://llrs.github.io

On BioConductor:BioCor-1.31.0(bioc 3.21)BioCor-1.30.0(bioc 3.20)

statisticalmethod clustering geneexpression network pathways networkenrichment systemsbiology bioconductor-packages bioinformatics functional-similarity gene gene-sets pathway-analysis similarity similarity-measurement

6.59 score 14 stars 374 downloads 26 exports 53 dependencies

Last updated 3 months agofrom:59fbed3856. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 28 2025
R-4.5-win	NOTE	Jan 28 2025
R-4.5-mac	WARNING	Jan 28 2025
R-4.5-linux	NOTE	Jan 28 2025
R-4.4-win	NOTE	Jan 28 2025
R-4.4-mac	NOTE	Jan 28 2025
R-4.3-win	NOTE	Jan 28 2025
R-4.3-mac	NOTE	Jan 28 2025

Dependencies:annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData glue graph GSEABase httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix memoise mime openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors snow sys UCSC.utils vctrs XML xtable XVector

About BioCor

Lluís Revilla, Juan José Lozano, Pau Sancho-Bru

Rendered fromBioCor_1_basics.Rmdusingknitr::rmarkdownon Jan 28 2025.

Last update: 2023-03-17
Started: 2018-02-28

Advanced usage of BioCor

Lluís Revilla, Juan José Lozano, Pau Sancho-Bru

Rendered fromBioCor_2_advanced.Rmdusingknitr::rmarkdownon Jan 28 2025.

Last update: 2023-03-17
Started: 2018-02-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
BioCor: A package to calculate functional similarities	BioCor-package BioCor
Additive integration of similarities	addSimilarities
Insert a matrix into another	AintoB
Similarity score between clusters of genes based on genes similarity	clusterGeneSim clusterGeneSim,character,character,GeneSetCollection-method
Similarity score between clusters of genes based on pathways similarity	clusterSim clusterSim,character,character,GeneSetCollection-method
i-th combination of n elements taken from r	combinadic
Combining values	combineScores combineScoresPar
Combine different sources of pathways	combineSources
Convert the similarities formats	conversions D2J J2D
Compare pathways	diceSim
Finds the indices of the duplicated events of a vector	duplicateIndices
Similarity score genes based on pathways similarity	geneSim geneSim,character,character,GeneSetCollection-method
Invert a list	inverseList
Similarity score between clusters of genes based on genes similarity	mclusterGeneSim mclusterGeneSim,list,GeneSetCollection-method
Similarity score between clusters of genes based on pathways similarity	mclusterSim mclusterSim,list,GeneSetCollection-method
Similarity score genes based on pathways similarity	mgeneSim mgeneSim,character,GeneSetCollection-method mgeneSim,missing,GeneSetCollection-method
Calculates the Dice similarity between pathways	mpathSim mpathSim,character,GeneSetCollection,ANY-method mpathSim,missing,GeneSetCollection,ANY-method mpathSim,missing,list,ANY-method mpathSim,missing,list,missing-method
Calculates the Dice similarity between pathways	pathSim pathSim,character,character,GeneSetCollection-method
The position of the nodes is based on the similarity between them.	plot_data plot_similarity
Remove duplicated rows and columns	removeDup
Transforms a vector to a symmetric matrix	seq2mat
Apply a function to a list of similarities	similarities
Weighted operations	weighted weighted.prod weighted.sum