Package: PanomiR 1.9.0

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]

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PanomiR.pdf |PanomiR.html✨
PanomiR/json (API)
NEWS

# 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-1.9.0(bioc 3.20)PanomiR-1.8.0(bioc 3.19)

bioconductor-package

11 exports 0.61 score 152 dependencies

Last updated 2 months agofrom:b2155cec94

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

Dependencies:annotate AnnotationDbi ape aplot askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli clusterProfiler codetools colorspace cowplot cpp11 crayon curl data.table DBI DEoptimR digest DOSE downloader dplyr enrichplot fansi farver fastmap fastmatch fgsea forcats formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggtree glue GO.db GOSemSim graph graphlayouts gridExtra gridGraphics GSEABase gson gtable HDO.db httr igraph IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle limma magrittr MASS mathjaxr Matrix MatrixModels memoise metap mgcv mime mnormt multcomp multtest munsell mutoss mvtnorm nlme numDeriv openssl org.Hs.eg.db patchwork pillar pkgconfig plogr plotrix plyr png polyclip preprocessCore purrr qqconf quantreg qvalue R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reshape2 rlang robustbase RSQLite S4Vectors sandwich scales scatterpie shadowtext sn snow SparseM statmod stringi stringr survival sys systemfonts TFisher TH.data tibble tidygraph tidyr tidyselect tidytree treeio tweenr UCSC.utils utf8 vctrs viridis viridisLite withr XML xtable XVector yulab.utils zlibbioc zoo

miRNA and pathway analysis with PanomiR

Pourya Naderi, Alan Teo, Ilya Sytchev, and Winston Hide

Rendered fromPanomiR.Rmdusingknitr::rmarkdownon Jun 17 2024.

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