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INSPEcT (version 1.2.2)

Analysis of 4sU-seq and RNA-seq time-course data

Description

INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.

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Version

Version

1.2.2

License

GPL-2

Maintainer

Stefano de Pretis

Last Published

February 15th, 2017

Functions in INSPEcT (1.2.2)

AIC-INSPEcT-method

Akaike information criterion calculated for the models evaluated by INSPEcT

dim,INSPEcT-method

Dimensions of an Object of Class INSPEcT

INSPEcT package

Plot the pre-modeled and modeled profiles for one gene

An S4 class to contain all rates and models generated by INSPEcT

Generate an object of class INSPEcT_diffsteady from two objects of class INSPEcT

Get and set number parameters for the modeling

An INSPEcT object with evaluated and modeled rates and concentrations

Calculate RPKM and count values on introns and exons from bam/sam files

Launch the modeling process

Get or replace INSPEcT_model object within INSPEcT object

Get the number of genes within the INSPEcT object

Display rate classification performance with thresholds visible at x-axis

Get the number of time points within the INSPEcT object

An INSPEcT_model object of 1000 simulated rates

intron, exons RPKM values of 500 genes from 4sU-seq and RNA-seq experiments

Display rate classification performance

Accessor to the slot totalSF of an INSPEcT object

Create a new INSPEcT object

A nice plot to see scaling factors used for RNA-seq and 4sU-seq libraries

Build the synthetic rates shaped on a dataset

INSPEcT_diffsteady-class

An S4 class to represent comparisons between two steady-state conditions

UCSC_mm9_genes_exons

A Gtf file containing exons definition of 100 genes

remove modelling information from INSPEcT object

Extract Parts of an INSPEcT or an INSPEcT_model Object

Heatmap that represent the fold changes of all the five features

Get or set parameters for model test and selection

ratesFirstGuessVar

Retrieve pre-modeling rates and concentrations variance

Divide an INSPEcT Object into groups

Generate synthetic rates and concentrations

Retrieve results of log likelihood test

UCSC_mm9_genes_introns

A Gtf file containing introns definition of 100 genes

INSPEcT_model-class

An S4 class to represent models generated by INSPEcT

Combine different Objects of Class INSPEcT

featureNames,INSPEcT-method

Gene Names Associated with an Object of Class INSPEcT

Accessor to the slot labeledSF of an INSPEcT object

An INSPEcT object with 1000 simulated rates and concentration and their modeled rates

An INSPEcT object with 1000 simulated rates and concentration and their modeled rates

Retrieve a single p-value for each rate

Retrieve the modeled rates and concentrations

Accessor to the slot tpts of an INSPEcT object

Retrieve the regulatory class for each gene

Calculate modeled rates and concentrations

Retrieve all results of chi-squared test

ratesFirstGuess

Retrieve pre-modeling rates and concentrations

Retrieve results of chi-squared test for the selected models

MA-plot from base means and log fold changes