grandR0.2.7 package

Analysis table functions

Gene set analysis

Apply a function over contrasts

Create Seurat object from a grandR object

Uses the kinetic model to calibrate the effective labeling time.

Calibrate the effective labeling time by matching half-lives to a .ref...

Internal functions to check for a valid analysis or slot names.

Build the type column for the gene info table.

Get the column annotation table or add additional columns to it

Compute statistics for all columns (i.e. samples or cells)

Expression percentage computation

Compute and evaluate functions for non constant rates

Compute NTR quantiles

Compute pseudo NTRs from two count matrices

Steady state half-lives for each sample

Compute summary statistics

Total expression computation

Get or set the conditions in the column annotation table.

Correct for 4sU dropout

Create Convolution Table from a Seurat object

Convencience methods for creating QC pdfs

Create Pseudobulk Table from a Seurat object

Internal function to apply functions to all slots etc.

Get or set the default slot for a grandR object.

Defer calling a function

Density estimation in 2d

Compute the Bayesian information criterion (BIC)

A list of predefined names for design vectors

Build the design semantics list

Perform 4sU dropout tests

Estimate 4sU dropout percentages

Estimate dispersion parameters for a count matrix using DESeq2

Estimate regulation from snapshot experiments

Function to compute the abundance of new or old RNA at time t for non-...

Function to compute the abundance of new or old RNA at time t for non-...

Functions to compute the abundance of new or old RNA at time t.

Filter genes

Find equivalent no4sU samples for 4sU samples

Obtain reference columns (samples or cells) for all columns (samples o...

Fit kinetic models to all genes.

Fit a kinetic model according to non-linear least squares.

Fit a kinetic model using a linear model.

Fit a kinetic model using the degradation rate transformed NTR posteri...

Compute the posterior distributions of RNA synthesis and degradation f...

Fit kinetics using pulseR

Fits RNA kinetics from snapshot experiments

Formatting function for correlations

Get the gene annotation table or add additional columns to it

Gene and sample (or cell) names

Internal functions to parse mode.slot strings

Obtain a table of analysis results values

Create a contrast matrix

Obtain a tidy table of values for a gene or a small set of genes

Describe parameters relevant to diagnostics

Obtain a genes x values table as a large matrix

Create a contrast matrix for two given conditions

Significant genes

Create a summarize matrix

Obtain a genes x values table

Create a grandR object and retrieve basic information

Checks for parallel execution

Estimation of log2 fold changes

Compute a likelihood ratio test.

List available gene sets

Extract an annotation table from a formatted names vector

Make an MA plot

Normalization

Normalization to a baseline

Log2 fold changes and Wald tests for differential expression

Perform Wald tests for differential expression

Convenience function to make the same type of plot for multple analyse...

Diagnostic plot for conversion frequencies

Plot gene values as bars

Plot gene groups as points

Gene plot comparing old vs new RNA

Plot progressive labeling timecourses

Gene plot for snapshot timecourse data

Gene plot comparing total RNA vs the NTR

Create heatmaps from grandR objects

Diagnostic plot for mismatch position for columns (by sample)

Diagnostic plot for mismatch position for columns (by mismatch type)

Diagnostic plot for estimated models (global conversion rate)

Diagnostic plot for estimated models (global error rate)

Diagnostic plot for estimated models (global error rate)

Diagnostic plot for estimated models (log likelihoods)

Diagnostic plot for estimated models (global NTR)

Diagnostic plot for estimated models (global conversion rate)

Diagnostic plot for estimated models (global error rate)

Diagnostic plot for estimated models (4sU increase)

Diagnostic plot for estimated models (global NTR)

Diagnostic plot for estimated models (global shape parameter)

Make a PCA plot

Diagnostic plot for estimated models (global error rate)

Stored plot functions

Make a scatter plot

Plot simulated data

Plot the distribution of gene types

Pool reads across columns

Parallel (s/l)apply

Read a count table

Read featureCounts

Read the output of GRAND-SLAM 2.0 into a grandR object.

Read the output of GRAND-SLAM 3.0 into a grandR object.

Read sparse new/total matrices

Create a renamer function

Rotate x axis labels

Copy the NTR slot and save under new name

Scale data

Semantics for concentration columns

Semantics for time columns

Serve a shiny web interface

Set up parallel execution

Simulate the kinetics of old and new RNA for given parameters.

Simulate metabolic labeling - nucleotide conversion RNA-seq data.

Simulate a complete time course of metabolic labeling - nucleotide con...

Simulate a complete time course of metabolic labeling - nucleotide con...

Slot functions

Convert a structure into a vector

Summarize a data matrix

Obtain the indices of the given genes

Transformations for PlotHeatmap

Estimate parameters for a one-shot experiment.

Update symbols using biomaRt

Use the given slot as NTR (is overwritten!)

Make a Vulcano plot

Perform Wilcoxon tests for differential expression