Package: SMITE 1.40.0

Neil Ari Wijetunga

SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.

Authors:Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally

SMITE_1.40.0.tar.gz
SMITE_1.40.0.zip(r-4.7-any)SMITE_1.40.0.zip(r-4.6-any)SMITE_1.40.0.zip(r-4.5-any)
SMITE_1.40.0.tgz(r-4.6-any)SMITE_1.40.0.tgz(r-4.5-any)
SMITE_1.40.0.tar.gz(r-4.7-any)SMITE_1.40.0.tar.gz(r-4.6-any)
SMITE_1.40.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SMITE/json (API)

# Install 'SMITE' in R:

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

Bug tracker:https://github.com/greallylab/smite/issues

Datasets:

expression_curated - A toy dataset ofcurated RNA-seq to test within SMITE
genes - A small set of RefSeq genes for converting
h3k4me1 - A toy dataset of H3k4me1 peaks to test within SMITE
hg19_genes - A bed file annotating Refseq genes for the hg19 genome build
methylation - A toy dataset of DNA methylation to test within SMITE
REACTOME - An Igraph network for REACTOME with nodes as gene symbols
test_annotation - A toy PvalueAnnotation

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

immunooncology differentialmethylation differentialexpression systemsbiology networkenrichment genomeannotation network sequencing rnaseq coverage

4.35 score 1 stars 16 scripts 610 downloads 7 mentions 24 exports 141 dependencies

Last updated from:c2a9ae00d5 (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	320
linux-devel	OK	541
source / vignettes	OK	433
linux-release	OK	524
macos-release	OK	271
macos-oldrel	OK	373
windows-devel	OK	594
windows-release	OK	642
windows-oldrel	OK	524
wasm-release	OK	293

Exports:addShadowText annotateExpression annotateModification convertGeneIds extractExpression extractGOseq extractModification extractModSummary extractModules extractScores highScores makePvalueAnnotation makePvalueObject normalizePval plotCompareScores plotDensityPval plotModule removeModification runBioNet runGOseq runSpinglass scorePval searchGOseq stoufferTest

Dependencies:abind AnnotationDbi askpass backports base64enc BH BiasedUrn Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt BioNet Biostrings bit bit64 bitops blob bslib cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray digest dplyr evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options geneLenDataBase generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue GO.db goseq graph gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime nlme nnet openssl org.Hs.eg.db pillar pkgconfig plyr png prettyunits progress purrr R6 rappdirs RBGL RColorBrewer Rcpp RCurl reactome.db restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 vctrs viridisLite withr xfun XML xml2 XVector yaml

SMITE Vignette

Rendered fromSMITE.Rmdusingknitr::rmarkdown

Last update: 2020-01-30
Started: 2016-02-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Significance-based Modules Integrating the Transcriptome and Epigenome	SMITE-package SMITE
Add shadow text (a second color bordering the text) to a plot	addShadowText addShadowText,ANY-method
Adding expression data to a PvalueAnnotation	annotateExpression annotateExpression,PvalueAnnotation-method
Adding modification data to a PvalueAnnotation	annotateModification annotateModification,PvalueAnnotation-method
Convert between gene ids	convertGeneIds convertGeneIds,character,character,character-method
A toy dataset ofcurated RNA-seq to test within SMITE	curated_expressiondata expression_curated
View the expression data stored in a PvalueAnnotation	extractExpression extractExpression,PvalueAnnotation-method
View the GOseq pathway analysis after having run Goseq, or search for a term.	extractGOseq extractGOseq,PvalueAnnotation-method searchGOseq searchGOseq,PvalueAnnotation-method
Extract some or all loaded modifications or a the summary of combined effects	extractModification extractModification,PvalueAnnotation-method extractModSummary extractModSummary,PvalueAnnotation-method
View specific modules within a PvalueAnnotation	extractModules extractModules,PvalueAnnotation-method
Extract scores for all genes	extractScores extractScores,PvalueAnnotation-method
A small set of RefSeq genes for converting	genes genes_for_conversiontest
A bed file annotating Refseq genes for the hg19 genome build	hg19_genes hg19_genes_bed
Generate a vector of the highest scoring genes	highScores highScores,PvalueAnnotation-method
A toy dataset of H3k4me1 peaks to test within SMITE	h3k4me1 histone_h3k4me1
Initialize a PvalueAnnotation	makePvalueAnnotation makePvalueAnnotation,ANY-method
Function to make a PvalueObject within a PvalueAnnotation	makePvalueObject makePvalueObject,PvalueAnnotation-method
A toy dataset of DNA methylation to test within SMITE	methylation methylationdata
This function normalizes p-values (Scores) that are otherwise on different scales.	normalizePval normalizePval,PvalueAnnotation-method
Compare two genomic features by score and display them in a hexbin plot	plotCompareScores plotCompareScores,PvalueAnnotation-method
Plot the density of the combined scores stored in a PvalueObject	plotDensityPval plotDensityPval,PvalueAnnotation-method
Plot a specific module after running Spinglass algorithm	plotModule plotModule,PvalueAnnotation-method
An Igraph network for REACTOME with nodes as gene symbols	REACTOME Reactome.Symbol.Igraph
A function to "unload" a modification that has already been added.	removeModification removeModification,PvalueAnnotation-method
Perform BioNet Analysis on a PvalueAnnotation	runBioNet runBioNet,PvalueAnnotation-method
Run a GoSeq pathway analysis	runGOseq runGOseq,PvalueAnnotation-method
Run Spinglass algorithm on a Scored PvalueAnnotation	runSpinglass runSpinglass,PvalueAnnotation-method
Making a single combined score for each gene	scorePval scorePval,PvalueAnnotation-method
Stouffer's Test	stoufferTest stoufferTest,vector-method
A toy PvalueAnnotation	test_annotation test_annotation_score_data