Package: mirTarRnaSeq 1.15.0

Mercedeh Movassagh

mirTarRnaSeq: mirTarRnaSeq

mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments.

Authors:Mercedeh Movassagh [aut, cre], Sarah Morton [aut], Rafael Irizarry [aut], Jeffrey Bailey [aut], Joseph N Paulson [aut]

mirTarRnaSeq_1.15.0.tar.gz
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mirTarRnaSeq.pdf |mirTarRnaSeq.html✨
mirTarRnaSeq/json (API)
NEWS

# Install 'mirTarRnaSeq' in R:
install.packages('mirTarRnaSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Combine - This is data is the mRNA expression across samples and miRNA expression data which is to be investigated in one file. This data set is used in documentation examples.
  • corr_0 - This is data is the mRNA FC and miRNA FC correlation data. This data set is used in documentation examples.
  • final_results - This is data is the mRNA FC and miRNA FC correlation/interaction data results after filteration. This data set is used in documentation examples.
  • geneVariant - This is data is the mRNA expression across samples and miRNA expression data which is to be investigated giving directions on which data is miRNA and which is mRNA. This data set is used in documentation examples.
  • inter0 - This is data is the mRNA FC and miRNA FC correlation/interaction original data. This data set is used in documentation examples.
  • mRNA - This is data is the mRNA expression file. This data set is used in documentation examples.
  • mRNA0_2 - This is data is the mRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.
  • mRNA0_5 - This is data is the mRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.
  • mRNA2_5 - This is data is the mRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.
  • mRNA_fc - This is data is the combined mRNA FC for all time points. This data set is used in documentation examples.
  • mRNA_fc2 - This data is the mRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.
  • miRNA - This is data is the miRNA expression file. This data set is used in documentation examples.
  • miRNA0_2 - This is data is the miRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.
  • miRNA0_5 - This is data is the miRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.
  • miRNA2_5 - This is data is the miRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.
  • miRNA_fc - This is data is the combined miRNA FC for all time points. This data set is used in documentation examples.
  • miRNA_fc2 - This data is the miRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.
  • miRanda - This is data is the results file from EBV miRanda getInputSpecies function. This data set is used in documentation examples.
  • miRandaM - This is data is the results file from mouse miRanda getInputSpecies function. This data set is used in documentation examples.
  • outs - This is data is the output file resulted from time point/conditions background correlation model. This data set is used in documentation examples.
  • outs2 - This is data is the output file resulted from time point/conditions background difference/interelation model. This data set is used in documentation examples.
  • results - This is data is the output file resulted from time point or conditions or correlation or interrelation model. This data set is used in documentation examples.
  • sig_InterR - This is data is the output file resulted from time point or conditions experiment for interrelation model after filtering and threshold modification. This data set is used in documentation examples.
  • sig_corrs - This is data is the output file resulted from time point or conditions experiment for correlation model after filtering and threshold modification. This data set is used in documentation examples.
  • some_model - This is data is the results file from regression analysis and its estimates. This data set is used in documentation examples.

On BioConductor:mirTarRnaSeq-1.13.0(bioc 3.20)mirTarRnaSeq-1.12.0(bioc 3.19)

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

mirnaregressionsoftwaresequencingsmallrnatimecoursedifferentialexpression

4.00 score 8 scripts 152 downloads 45 exports 49 dependencies

Last updated 23 days agofrom:60572a9568. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:combinercorMirnaRnacorMirnaRnaMirandadrawCorPlotdrawInterPlotsfdrSigfinInterResultgeneVarigetInputSpeciesglm_gaussianglm_multiglm_nbglm_poissonglm_zeroinflglm_zeroinfl_negbinglm_zeroinfl_poissonmiRanCompmiranda_sponge_predictmiRandaIntersectmirandaIntersectIntermirRnaDensityCormirRnaDensityIntermirRnaHeatmapmirRnaHeatmapDiffmodelAICmodelCoefficientsmodelDatamodelModelNamemodelModelPvaluemodelsFiltermodelTermPvaluesone2manySpongeone2OneRnaMiRNAplotFitplotResidualsplotTermsrunAllMirnaModelsrunModelrunModelssampCorRnaMirnathreshSigthreshSigIntertwoTimePointtwoTimePointSamptzTrans

Dependencies:assertthatbitopscaToolsclicolorspacecorrplotdata.tabledplyrfansifarvergenericsggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepheatmappillarpkgconfigplyrpsclpurrrR.methodsS3R.ooR.utilsR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbletidyselectutf8vctrsviridisviridisLitewithr

mirTarRnaSeq

Mercedeh Movassagh

Rendered frommirTarRnaSeq.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-04-06
Started: 2021-02-23

Readme and manuals

Help Manual

Help pageTopics
Decifer a 'model parameter' and run appropriate 'glm_...' function.canonicalModel_
This is data is the mRNA expression across samples and miRNA expression data which is to be investigated in one file. This data set is used in documentation examples.Combine
combiner combines the miRNA and mRNA filescombiner
corMirnaRna correlation for miRNA and mRNAcorMirnaRna
corMirnaRnaMiranda correlation for miRNA and mRNAcorMirnaRnaMiranda
This is data is the mRNA FC and miRNA FC correlation data. This data set is used in documentation examples.corr_0
downloadMirandaFile Read internal Miranda filedownloadMirandaFile
drawCorPlot correlation plots for mRNA and miRNA regression resultsdrawCorPlot
drawInterPlots for finInterResult miRNA and mRNA Interrelation real datadrawInterPlots
fdrSig Ruturns FDR significant miRNA/mRNA predictionsfdrSig
This is data is the mRNA FC and miRNA FC correlation/interaction data results after filteration. This data set is used in documentation examples.final_results
finInterResult miRNA and mRNA interrelation in two-time points results in a dataframe.finInterResult
geneVari Makes a list of gene names to be used in the runModels functiongeneVari
This is data is the mRNA expression across samples and miRNA expression data which is to be investigated giving directions on which data is miRNA and which is mRNA. This data set is used in documentation examples.geneVariant
Return Miranda data for a given species.getInputSpecies
Model functions for GLM with Gaussian model.glm_gaussian
Model functions for GLM with negative binomial family.glm_multi
Model functions for GLM with negative binomial family.glm_nb
Model functions for GLM with Poisson model.glm_poisson
Model functions for zero inflated model using either Poisson or Negative Binomial distributions.glm_zeroinfl
alias for glm_zeroinfl("negbin")glm_zeroinfl_negbin
alias for glm_zeroinfl("poisson")glm_zeroinfl_poisson
importMirandaFile Read internal Miranda fileimportMirandaFile
This is data is the mRNA FC and miRNA FC correlation/interaction original data. This data set is used in documentation examples.inter0
makeFormulaRightSide makes right hand side of formula for model variables: vector of indep. variablesmakeFormulaRightSide
miRanComp comparison of mRNAs present with miRanda file targetsmiRanComp
This is data is the results file from EBV miRanda getInputSpecies function. This data set is used in documentation examples.miRanda
Transform miRanda data for relevant mRNA and miRNA to matrix form compatible with spongemiranda_sponge_predict
miRandaIntersect Looks for Intersection of Significant output results with miRanda Results from getInputSpeciesDF functionmiRandaIntersect
mirandaIntersectInter Looks for Intersection of Significant output results with miRanda Results from getInputSpeciesDF functionmirandaIntersectInter
This is data is the results file from mouse miRanda getInputSpecies function. This data set is used in documentation examples.miRandaM
This is data is the miRNA expression file. This data set is used in documentation examples.miRNA
This is data is the combined miRNA FC for all time points. This data set is used in documentation examples.miRNA_fc
This data is the miRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.miRNA_fc2
This is data is the miRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.miRNA0_2
This is data is the miRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.miRNA0_5
This is data is the miRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.miRNA2_5
mirRnaDensityCor for miRTarRNASeq miRNA and mRNA correlation real data versus sampled datamirRnaDensityCor
mirRnaDensityInter for mirTarRnaSeq miRNA and mRNA Interrelation real data versus sampled datamirRnaDensityInter
mirRnaHeatmap pheatmap for miRTarRNASeq miRNA and mRNA correlationmirRnaHeatmap
mirRnaHeatmapDiff heatmap for miRTarRNASeq miRNA and mRNA correlationmirRnaHeatmapDiff
Obtain model AICmodelAIC
Obtain coefficientsmodelCoefficients
Obtain model input datamodelData
Obtain model namemodelModelName
Obtain model p-valuemodelModelPvalue
modelsFilter Filter a list of models based on logical expressionmodelsFilter
Obtain p-values for terms in model formulamodelTermPvalues
This is data is the mRNA expression file. This data set is used in documentation examples.mRNA
This is data is the combined mRNA FC for all time points. This data set is used in documentation examples.mRNA_fc
This data is the mRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.mRNA_fc2
This is data is the mRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.mRNA0_2
This is data is the mRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.mRNA0_5
This is data is the mRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.mRNA2_5
Sparse Partial Correlations On mRNA/miRNA Expression We make mirTarRnaSeq compatible to SPONGE package in order to estimate sparse matrix correlation (using elstic net) for prediction potential miRNA-mRNA interaction. Note this function/method is suggested for miRNA/mRNA interactions in many samples with a notable variance of mRNA/miRNA expression. This model also only reports negative sparse partial correlation predictions.one2manySponge
one2OneRnaMiRNA correlation for miRNA and mRNA using differntial expression fold change and if/when available p-valueone2OneRnaMiRNA
This is data is the output file resulted from time point/conditions background correlation model. This data set is used in documentation examples.outs
This is data is the output file resulted from time point/conditions background difference/interelation model. This data set is used in documentation examples.outs2
Plot modelplotFit
Plot residualsplotResiduals
plotTermsplotTerms
This is data is the output file resulted from time point or conditions or correlation or interrelation model. This data set is used in documentation examples.results
runAllMirnaModels runModel for all miRNAsrunAllMirnaModels
Run a model of a specific kindrunModel
runModels runs miRNA mrna model model for various miRNA-mRNA data distributionsrunModels
sampCorRnaMirna sampling for correlation for miRNA and mRNAsampCorRnaMirna
This is data is the output file resulted from time point or conditions experiment for correlation model after filtering and threshold modification. This data set is used in documentation examples.sig_corrs
This is data is the output file resulted from time point or conditions experiment for interrelation model after filtering and threshold modification. This data set is used in documentation examples.sig_InterR
This is data is the results file from regression analysis and its estimates. This data set is used in documentation examples.some_model
threshSig Using shuffling threshold finds appropriate significant miRNA-mRNA correlationthreshSig
threshSigInter Using shuffling threshold finds appropriate significant miRNA-mRNA correlationthreshSigInter
twoTimePoint miRNA and mRNA interrelation in two timepointstwoTimePoint
twoTimePointSamp miRNA and mRNA interrelation in two timepoints samplingtwoTimePointSamp
tzTransTranspose and z-score transformationtzTrans