Package: PanomiR 1.11.0

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_1.11.0.tar.gz
PanomiR_1.11.0.zip(r-4.5)PanomiR_1.11.0.zip(r-4.4)PanomiR_1.11.0.zip(r-4.3)
PanomiR_1.11.0.tgz(r-4.4-any)PanomiR_1.11.0.tgz(r-4.3-any)
PanomiR_1.11.0.tar.gz(r-4.5-noble)PanomiR_1.11.0.tar.gz(r-4.4-noble)
PanomiR_1.11.0.tgz(r-4.4-emscripten)PanomiR_1.11.0.tgz(r-4.3-emscripten)
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'))

Peer review:

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)

geneexpressiongenesetenrichmentgenetargetmirnapathways

4.89 score 3 stars 13 scripts 154 downloads 11 exports 147 dependencies

Last updated 23 days agofrom:747888b4c7. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:clusterPlotdifferentialPathwayAnalysisgetDesignMatrixlinColumnFindermappingPathwaysClustersmiRNAPathwayEnrichmentpathwayGeneTabpathwaySummaryprioritizeMicroRNAreportEnrichmenttableFromGSC

Dependencies:annotateAnnotationDbiapeaplotaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemcliclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIDEoptimRdigestDOSEdplyrenrichplotfansifarverfastmapfastmatchfgseaforcatsformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgraphgridGraphicsGSEABasegsongtablehttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelimmamagrittrMASSmathjaxrMatrixMatrixModelsmemoisemetapmgcvmimemnormtmultcompmulttestmunsellmutossmvtnormnlmenumDerivopensslorg.Hs.eg.dbpatchworkpillarpkgconfigplogrplotrixplyrpngpolyclippreprocessCorepurrrqqconfquantregqvalueR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppEigenRdpackreshape2rlangrobustbaseRSQLiteS4VectorssandwichscalesscatterpiesnsnowSparseMstatmodstringistringrsurvivalsyssystemfontsTFisherTH.datatibbletidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectoryulab.utilszlibbioczoo

miRNA and pathway analysis with PanomiR

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

Rendered fromPanomiR.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
function to align a list of sets and a reference universealignToUniverse
Plots clusters of pathways with associated directionality.clusterPlot
Differential Expression Analysis For PathwaysdifferentialPathwayAnalysis
Pairwise enrichment analysis between two given lists of setsenrichAllPairs
Obtain Design MatrixgetDesignMatrix
function to get a DE tablegetDiffExpTable
function to get residuals with respect to a set of covariatesgetResidual
Example genesets from MSigDBgscExample
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 matrixlinColumnFinder
Outputs a table with pathways and their respective clustersmappingPathwaysClusters
Outputs a table with col x, miRNA, probability of observing k against a random distribution of the cover of methodologymethodProbBase
Readouts and datasets for minimal reproducible examples of the PanomiR.miniTestsPanomiR
Enrichment Probability Of miRNAsmiRNAPathwayEnrichment
Canonical pathways from Molecular Signatures Database, MsigDb V6.2msigdb_c2
A table of gene-pathway association. based on the pathways of MSigDB.path_gene_table
Pathway-Gene AssociationspathwayGeneTab
Pathway Summary StatisticspathwaySummary
Creates a network out of pcxn tablepcxnToNet
Prioritize miRNAprioritizeMicroRNA
Publication-ready miRNA-Pathway Enrichment tablereportEnrichment
Outputs a table of sampling data(rows are miRNA and cols are samples)samplingDataBase
Pathway-Gene Associations from GeneSet collectionstableFromGSC
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 familytargetScan_03