Package: INSPEcT 1.37.0

Stefano de Pretis

INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or steady-state conditions, with or without the support of nascent RNA data.

Authors:Stefano de Pretis

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

# Install 'INSPEcT' in R:

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

Datasets:

allcounts - A list containing mature and nascent counts for exons and introns, three replicates and 11 time points: 0,1/6,1/3,1/2,1,1.5,2,4,8,12,16 hours.
featureWidths - Contains two variables: "exWdths" and "intWdths" containing the lenght of the exons and introns, respectively, relative to the genes in "allcounts"
libsizes - Contains two variables: "nascentLS" and "totalLS" containing the sequencing depth of nascent and total libraries respectively, relative to the experiments in "allcounts"

On BioConductor:INSPEcT-1.37.0(bioc 3.21)INSPEcT-1.36.0(bioc 3.20)

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

sequencing rnaseq generegulation timecourse systemsbiology

4.56 score 9 scripts 342 downloads 6 mentions 59 exports 121 dependencies

Last updated 23 days agofrom:7d70bacb96. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	WARNING	Nov 18 2024
R-4.5-linux	WARNING	Nov 18 2024
R-4.4-win	WARNING	Nov 18 2024
R-4.4-mac	WARNING	Nov 18 2024
R-4.3-win	WARNING	Nov 18 2024
R-4.3-mac	WARNING	Nov 18 2024

Exports:AIC calculateDelta calculateRatePvals calculateTau chisqmodel chisqtest combine compareSteady compareSteadyNoNascent computeConfidenceIntervals convergence correlationPlot degradation featureNames featureNames<-geneClass inHeatmap inspectFromBAM inspectFromPCR labeledSF logLik makeModelRates makeOscillatorySimModel makeSimDataset makeSimModel mature modelingParams modelRates modelRatesNF modelSelection newINSPEcT nGenes nTpts plotGene plotMA plotPMgene plotPMtrend premature processing processingDelay PTratio PTreg quantifyExpressionsFromBAMs quantifyExpressionsFromBWs quantifyExpressionsFromTrAbundance quantifyExpressionsFromTrCounts ratePvals ratesFirstGuess ratesFirstGuessVar removeModel rocCurve rocThresholds runINSPEcTGUI show split synthesis tpts viewConfidenceIntervals viewModelRates

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib cachem cellranger cli codetools colorspace commonmark cpp11 crayon curl DBI DelayedArray DESeq2 deSolve digest fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable hms htmltools httpuv httr IRanges isoband jquerylib jsonlite KEGGREST KernSmooth labeling lambda.r later lattice lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plgem plogr plyr png prettyunits pROC progress promises R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl readxl rematch restfulr Rhtslib rjson rlang rootSolve Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales shiny snow sourcetools SparseArray SummarizedExperiment sys tibble TxDb.Mmusculus.UCSC.mm9.knownGene UCSC.utils utf8 vctrs viridisLite withr XML xtable XVector yaml zlibbioc

INSPEcT - INference of Synthesis, Processing and dEgradation rates from Transcriptomic data

de Pretis S., Furlan M., Pelizzola M.

Rendered fromINSPEcT.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2020-04-08
Started: 2019-09-23

INSPEcT-GUI

de Pretis S., Furlan M., Pelizzola M.

Rendered fromINSPEcT_GUI.rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2020-02-03
Started: 2019-12-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Akaike information criterion calculated for the models evaluated by INSPEcT	AIC,INSPEcT-method AIC,INSPEcT_model-method AIC-INSPEcT-method
A list containing mature and nascent counts for exons and introns, three replicates and 11 time points: 0,1/6,1/3,1/2,1,1.5,2,4,8,12,16 hours.	allcounts
Calculate a single p-value for each rate	calculateRatePvals calculateRatePvals,INSPEcT-method
Retrieve results of chi-squared test for the selected models	chisqmodel chisqmodel,INSPEcT-method
Retrieve all results of chi-squared test	chisqtest chisqtest,INSPEcT-method chisqtest,INSPEcT_model-method
Combine different Objects of Class INSPEcT	combine combine,INSPEcT,INSPEcT-method
Generate an object of class INSPEcT_diffsteady from an object of class INSPEcT	compareSteady compareSteady,INSPEcT-method
Identify post-transcriptionally regulated genes from an object of class INSPEcT_diffsteady	compareSteadyNoNascent compareSteadyNoNascent,INSPEcT_steadyNoNascent-method
Compute confidence intervals	computeConfidenceIntervals computeConfidenceIntervals,INSPEcT-method
Retrieve the convergence for the selected models of each gene	convergence convergence,INSPEcT-method
Display rate classification performance	correlationPlot correlationPlot,INSPEcT_model,INSPEcT-method
Dimensions of an Object of Class INSPEcT	dim,INSPEcT-method
Extract Parts of an INSPEcT or an INSPEcT_model Object	Extract [,INSPEcT,ANY,ANY,ANY-method [,INSPEcT_diffsteady,ANY,ANY,ANY-method [,INSPEcT_model,ANY,ANY,ANY-method
Gene Names Associated with an Object of Class INSPEcT	featureNames,INSPEcT-method featureNames<-,INSPEcT-method
Contains two variables: "exWdths" and "intWdths" containing the lenght of the exons and introns, respectively, relative to the genes in "allcounts"	featureWidths
Retrieve the regulatory class for each gene	geneClass geneClass,INSPEcT-method geneClass,INSPEcT_diffsteady-method geneClass,INSPEcT_model-method
Heatmap that represent the fold changes of all the five features	inHeatmap inHeatmap,INSPEcT-method
INSPEcT package	INSPEcT
An S4 class to represent comparisons between two steady-state conditions	degradation degradation,INSPEcT_diffsteady-method featureNames,INSPEcT_diffsteady-method INSPEcT_diffsteady-class processing processing,INSPEcT_diffsteady-method show,INSPEcT_diffsteady-method synthesis synthesis,INSPEcT_diffsteady-method
An S4 class to represent models generated by INSPEcT	INSPEcT_model-class show,INSPEcT_model-method
An S4 class to represent steady-state analysis without nascent RNA	INSPEcT_steadyNoNascent-class show,INSPEcT_steadyNoNascent-method [,INSPEcT_steadyNoNascent,ANY,ANY,ANY-method
An S4 class to contain all rates and models generated by INSPEcT	INSPEcT-class show,INSPEcT-method
Run shiny applications contained in the package INSPEcT	INSPEcT-shinyApps runINSPEcTGUI runProcessingRateDelay
Wrapper function from BAM files	inspectFromBAM
Wrapper function from PCR quantifications	inspectFromPCR
Accessor to the slot labeledSF of an INSPEcT object	labeledSF labeledSF,INSPEcT-method
Contains two variables: "nascentLS" and "totalLS" containing the sequencing depth of nascent and total libraries respectively, relative to the experiments in "allcounts"	libsizes
Retrieve results of log likelihood test	logLik logLik,INSPEcT-method logLik,INSPEcT_model-method
Calculate modeled rates and concentrations	makeModelRates makeModelRates,INSPEcT-method makeModelRates,INSPEcT_model-method
Build the synthetic rates with oscillatory pattern	makeOscillatorySimModel makeOscillatorySimModel,INSPEcT-method
Generate synthetic rates and concentrations	makeSimDataset makeSimDataset,INSPEcT_model-method
Build the synthetic rates shaped on a dataset	makeSimModel makeSimModel,INSPEcT-method
Get mature RNA expressions from an object of class INSPEcT_diffsteady	mature mature,INSPEcT_steadyNoNascent-method
Get mature RNA expressions variances from an object of class INSPEcT_diffsteady	matureVar matureVar,INSPEcT_steadyNoNascent-method
Get and set number parameters for the modeling	modelingParams modelingParams,INSPEcT-method
Launch the modeling process	modelRates modelRates,INSPEcT-method
Launch the modeling process without imposing sigmoid/impulse functional form	modelRatesNF modelRatesNF,INSPEcT-method
Visualize criteria used for rate variability	modelSelection modelSelection,INSPEcT-method modelSelection,INSPEcT_model-method
Create a new INSPEcT object	newINSPEcT
Get the number of genes within the INSPEcT object	nGenes nGenes,INSPEcT-method
Get the number of time points within the INSPEcT object	nTpts nTpts,INSPEcT-method
Plot the pre-modeled and modeled profiles for one gene	plotGene plotGene,INSPEcT-method
MA-plot from base means and log fold changes	plotMA plotMA,INSPEcT_diffsteady-method
Plot the premature/mature expression of a gene and the global trend from an object of class INSPEcT_diffsteady	plotPMgene plotPMgene,INSPEcT_steadyNoNascent-method
Plot the premature/mature trend from an object of class INSPEcT_diffsteady	plotPMtrend plotPMtrend,INSPEcT_steadyNoNascent-method
Get premature RNA expressions from an object of class INSPEcT_diffsteady	premature premature,INSPEcT_steadyNoNascent-method
Get premature RNA expressions variances from an object of class INSPEcT_diffsteady	prematureVar prematureVar,INSPEcT_steadyNoNascent-method
Classify genes as delayed by the processing using the delta and tau metrics	calculateDelta calculateDelta,INSPEcT-method calculateTau calculateTau,INSPEcT-method processingDelay processingDelay,INSPEcT-method
Calculate post-transcriptional ratio from an object of class INSPEcT_diffsteady	PTratio PTratio,INSPEcT_steadyNoNascent-method
Calculate the post-transcriptional ratio from an object of class INSPEcT_diffsteady	PTreg PTreg,INSPEcT_steadyNoNascent-method
Evaluate introns and exons expressions from BAM or SAM files	quantifyExpressionsFromBAMs
Evaluate introns and exons expressions from BAM or SAM files	quantifyExpressionsFromBWs
Given introns and exons abundances (for example RPKMs) this method returns their variances evaluated thorugh plgem.	quantifyExpressionsFromTrAbundance
Evaluates introns and exons RPKMs, per gene, from counts data.	quantifyExpressionsFromTrCounts
Retrieve a single p-value for each rate	ratePvals ratePvals,INSPEcT-method
Retrieve pre-modeling rates and concentrations	ratesFirstGuess ratesFirstGuess,INSPEcT-method
Retrieve pre-modeling rates and concentrations variance	ratesFirstGuessVar ratesFirstGuessVar,INSPEcT-method
remove modelling information from INSPEcT object	removeModel removeModel,INSPEcT-method
Display rate classification performance	rocCurve rocCurve,INSPEcT_model,INSPEcT-method
Display rate classification performance with thresholds visible at x-axis	rocThresholds rocThresholds,INSPEcT_model,INSPEcT-method
Set confidence intervals	setConfidenceIntervals setConfidenceIntervals,INSPEcT-method
An INSPEcT object with 1000 simulated rates and concentration and their modeled rates	simData3rep_Nascent
An INSPEcT object with 1000 simulated rates and concentration and their modeled rates	simData3rep_NoNascent
An INSPEcT object with 1000 simulated rates and concentration and their modeled rates	simData4rep_Nascent
An INSPEcT object with 1000 simulated rates and concentration and their modeled rates	simData4rep_NoNascent
Divide an INSPEcT Object into groups	split split,INSPEcT,ANY-method
Accessor to the slot tpts of an INSPEcT object	tpts tpts,INSPEcT-method
Retrieve the modeled Confidence Intervals	viewConfidenceIntervals viewConfidenceIntervals,INSPEcT-method
Retrieve the modeled rates and concentrations	viewModelRates viewModelRates,INSPEcT-method