Package: PanomiR 1.17.0

Pourya Naderi

PanomiR: Detection of miRNAs that regulate interacting groups of pathways

PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.

Authors:Pourya Naderi [aut, cre], Yue Yang Teo [aut], Ilya Sytchev [aut], Winston Hide [aut]

PanomiR_1.17.0.tar.gz
PanomiR_1.17.0.zip(r-4.7)PanomiR_1.17.0.zip(r-4.6)PanomiR_1.17.0.zip(r-4.5)
PanomiR_1.17.0.tgz(r-4.6-any)PanomiR_1.17.0.tgz(r-4.5-any)
PanomiR_1.17.0.tar.gz(r-4.7-any)PanomiR_1.17.0.tar.gz(r-4.6-any)
PanomiR_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PanomiR/json (API)

# Install 'PanomiR' in R:

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

Bug tracker:https://github.com/pouryany/panomir/issues

Datasets:

gscExample - Example genesets from MSigDB
miniTestsPanomiR - Readouts and datasets for minimal reproducible examples of the PanomiR.
msigdb_c2 - Canonical pathways from Molecular Signatures Database, MsigDb V6.2
path_gene_table - A table of gene-pathway association. based on the pathways of MSigDB.
targetScan_03 - A processed list of miRNA target gene sets from the TargetScan dataset. Each list item is a list of genes targeted by the respective miRNA family

On BioConductor:PanomiR-1.17.0(bioc 3.24)PanomiR-1.16.0(bioc 3.23)

geneexpression genesetenrichment genetarget mirna pathways

4.98 score 3 stars 16 scripts 11 exports 155 dependencies

Last updated from:d0a6310a04. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	231
linux-devel-x86_64	OK	303
source / vignettes	OK	348
linux-release-x86_64	OK	254
macos-release-arm64	OK	149
macos-oldrel-arm64	OK	138
windows-devel	OK	132
windows-release	OK	147
windows-oldrel	OK	148
wasm-release	OK	218

Exports:clusterPlot differentialPathwayAnalysis getDesignMatrix linColumnFinder mappingPathwaysClusters miRNAPathwayEnrichment pathwayGeneTab pathwaySummary prioritizeMicroRNA reportEnrichment tableFromGSC

Dependencies:aisdk annotate AnnotationDbi ape aplot askpass base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem callr cli cluster clusterProfiler codetools cpp11 crayon curl DBI DEoptimR digest DOSE dplyr enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver forcats fs gdtools generics ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim graph gridGraphics GSEABase gson gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lattice lazyeval lifecycle limma magrittr MASS mathjaxr Matrix MatrixModels memoise metap mime mnormt multcomp multtest mutoss mvtnorm nlme numDeriv openssl org.Hs.eg.db otel patchwork pillar pkgconfig plotrix plyr png polyclip preprocessCore processx ps purrr qqconf quantreg qvalue R6 rappdirs rbibutils RColorBrewer Rcpp RcppEigen Rdpack reshape2 rlang rmarkdown robustbase RSQLite S4Vectors S7 sandwich sass scales scatterpie Seqinfo sn SparseM statmod stringi stringr survival sys systemfonts TFisher TH.data tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs viridisLite withr xfun XML xtable XVector yaml yulab.utils zoo

miRNA and pathway analysis with PanomiR

Rendered fromPanomiR.Rmdusingknitr::rmarkdown

Last update: 2022-08-17
Started: 2021-11-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
function to align a list of sets and a reference universe	alignToUniverse
Plots clusters of pathways with associated directionality.	clusterPlot
Differential Expression Analysis For Pathways	differentialPathwayAnalysis
Pairwise enrichment analysis between two given lists of sets	enrichAllPairs
Obtain Design Matrix	getDesignMatrix
function to get a DE table	getDiffExpTable
function to get residuals with respect to a set of covariates	getResidual
Example genesets from MSigDB	gscExample
Outputs a table with col x (miRNA), probability of observing k (depending on methodology) against a random distribution with jack-knifing of the pathway cluster (removing a pathway at a time)	jackKnifeBase
Function imported from https://github.com/th1vairam/CovariateAnalysis Modified from http://stackoverflow.com/questions/13088770/ Function to find linearly dependednt columns of a matrix	linColumnFinder
Outputs a table with pathways and their respective clusters	mappingPathwaysClusters
Outputs a table with col x, miRNA, probability of observing k against a random distribution of the cover of methodology	methodProbBase
Readouts and datasets for minimal reproducible examples of the PanomiR.	miniTestsPanomiR
Enrichment Probability Of miRNAs	miRNAPathwayEnrichment
Canonical pathways from Molecular Signatures Database, MsigDb V6.2	msigdb_c2
A table of gene-pathway association. based on the pathways of MSigDB.	path_gene_table
Pathway-Gene Associations	pathwayGeneTab
Pathway Summary Statistics	pathwaySummary
Creates a network out of pcxn table	pcxnToNet
Prioritize miRNA	prioritizeMicroRNA
Publication-ready miRNA-Pathway Enrichment table	reportEnrichment
Outputs a table of sampling data(rows are miRNA and cols are samples)	samplingDataBase
Pathway-Gene Associations from GeneSet collections	tableFromGSC
A processed list of miRNA target gene sets from the TargetScan dataset. Each list item is a list of genes targeted by the respective miRNA family	targetScan_03