Package: SIM 1.83.0

Renee X. de Menezes

SIM: Integrated Analysis on two human genomic datasets

Finds associations between two human genomic datasets.

Authors:Renee X. de Menezes and Judith M. Boer

# Install 'SIM' in R:

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

Datasets:

On BioConductor:SIM-1.83.0(bioc 3.24)SIM-1.82.0(bioc 3.23)

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

Last updated from:6fd83a1167. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	159
linux-devel-arm64	WARNING	197
linux-devel-x86_64	WARNING	274
source / vignettes	OK	209
linux-release-arm64	WARNING	208
linux-release-x86_64	WARNING	237
macos-release-arm64	WARNING	164
macos-release-x86_64	WARNING	272
macos-oldrel-arm64	WARNING	120
macos-oldrel-x86_64	WARNING	298
windows-devel	WARNING	197
windows-release	WARNING	177
windows-oldrel	WARNING	181
wasm-release	OK	132

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

Help page	Topics
Statistical Integration of Microarrays	SIM-package SIM
Array Comparative Genomic Hybridization data	acgh.data
Assemble the data to run the integrated analysis	assemble.data
Table with chromosome information	chrom.table
Expression data example	expr.data
Get the overlapping regions between independent and dependent regions	getoverlappingregions
Impute NA's in array-CGH data	impute.nas.by.surrounding
Integrated analysis of dependent and indepedent microarray data	integrated.analysis
Link a metadata annotation file to expression ID	link.metadata
Link RESOURCERER annotation file to expression ID	RESOURCERER.annotation.to.ID
Samples for example data	samples
P-value plot and mean-zscore plots with indication of overlapping features.	sim.plot.overlapping.indep.dep.features
Plot the P-values in whole genome overview	sim.plot.pvals.on.genome
P-value histograms and P-values along the genome per region	sim.plot.pvals.on.region
Zoom in on heatmap	sim.plot.zoom.in
Association heatmap from z-scores	sim.plot.zscore.heatmap
Update the chromomosome table	sim.update.chrom.table
Sums significant P-values for the analyzed regions	tabulate.pvals
Lists the P-values for the dependent features	tabulate.top.dep.features
Lists the mean z-scores for the independent features	tabulate.top.indep.features