Package: PANR 1.53.0

Xin Wang

PANR: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.

Authors:Xin Wang <[email protected]>

PANR_1.53.0.tar.gz
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PANR_1.53.0.tgz(r-4.4-any)PANR_1.53.0.tgz(r-4.3-any)
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PANR.pdf |PANR.html✨
PANR/json (API)
NEWS

# Install 'PANR' in R:

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

Datasets:

Bakal2007 - Rich morphological phenotypes for gene overexpression and RNA interference screens
Bakal2007Cluster - Rich morphological phenotypes for gene overexpression and RNA interference screens
bm1 - Rich morphological phenotypes for gene overexpression and RNA interference screens
nodeColor - Rich morphological phenotypes for gene overexpression and RNA interference screens

On BioConductor:PANR-1.53.0(bioc 3.21)PANR-1.52.0(bioc 3.20)

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

immunooncology networkinference visualization graphandnetwork clustering cellbasedassays

3.30 score 2 scripts 228 downloads 18 exports 22 dependencies

Last updated 2 months agofrom:a07182d954. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	NOTE	Dec 19 2024
R-4.5-linux	NOTE	Dec 19 2024
R-4.4-win	NOTE	Dec 19 2024
R-4.4-mac	NOTE	Dec 19 2024
R-4.3-win	NOTE	Dec 19 2024
R-4.3-mac	NOTE	Dec 19 2024

Exports:assoScore buildPAN cosineDist cosineSim exportPAN fitBM fitNULL infer p2SNR permNULL pvclustModule sigModules SNR2p summarize view viewLegend viewNestedModules viewPAN

Dependencies:cli colorspace cpp11 farver glue igraph labeling lattice lifecycle magrittr MASS Matrix munsell pkgconfig pvclust R6 RColorBrewer RedeR rlang scales vctrs viridisLite

Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations

Rendered fromPANR-Vignette.Rnwusingutils::Sweaveon Dec 19 2024.

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Association scores for gene pairs	assoScore
An S4 class for beta mixture modelling of functional gene associations	BetaMixture BetaMixture-class
Build an igraph or RedeR graph for PAN	buildPAN buildPAN,PAN,character_Or_missing,list_Or_missing,logical_Or_missing-method
Compute cosine similarities or distances between pairs of genes	cosineDist cosineSim
Rich morphological phenotypes for gene overexpression and RNA interference screens	Bakal2007 Bakal2007Cluster bm1 nodeColor
Export inferred PAN or module graphs to files	exportPAN exportPAN,PAN,character_Or_missing,character_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method
Fit a three-beta mixture model to densities of functional gene associations	fitBM fitBM,BetaMixture,list_Or_missing,list_Or_missing,logical_Or_missing-method
Fit the NULL component of a three-beta mixture model for functional gene associations	fitNULL fitNULL,BetaMixture,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,character_Or_missing,logical_Or_missing-method
Infer a posterior association network	infer infer,PAN,list,logical_Or_missing,logical_Or_missing-method
Translate p-values to Signal-to-Noise Ratios	p2SNR p2SNR,BetaMixture,numeric_Or_integer-method
An S4 class for inferring a posterior association network	PAN PAN-class
Search enriched functional gene modules by pvclust	pvclustModule pvclustModule,PAN,numeric_Or_integer_Or_missing,character_Or_missing,character_Or_missing,logical_Or_missing,logical_Or_missing-method
Retrieve ids for significant gene modules searched by pvclust	sigModules sigModules,PAN,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method
Translate p-values to Signal-to-Noise Ratios	SNR2p SNR2p,BetaMixture,numeric_Or_integer-method
Summarize the object of S4 class 'BetaMixture' or 'PAN'	summarize summarize,BetaMixture,character_Or_missing-method summarize,PAN,character_Or_missing-method
View the results of beta-mixture model fitting	view view,BetaMixture,character_Or_missing-method
View the legends for the graph built for PAN	viewLegend viewLegend,PAN,character_Or_missing-method
View the nested modules in a posterior association network in RedeR	viewNestedModules viewNestedModules,PAN,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,logical_Or_missing-method
Show posterior association networks or modules in `igraph' or `RedeR'	viewPAN viewPAN,PAN,character_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method