# Differential Pattern Analysis via Linear Modeling

## Documentation for package ‘DiPALM’ version 1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

DiPALM-package | DiPALM - Differential Pattern Analysis via Linear Modeling
AdjustPvalue | Determine p-values based on permutation test results
BlankPlot | Generate a blank plot window
BuildLimmaLM | Fit linear models to time-course expression patterns using the limma package
BuildModMembership | Calculate module membership (kME) for all genes in a time-course data set
col_format_sub | Substitute values in for the time, treatment, and replicate portion of a column format.
DiPALM | DiPALM - Differential Pattern Analysis via Linear Modeling
dipalm | Run a single instance of the DiPALM pipeline with replicates permuted.
exampleData | Example Data: Data for use with the DiPALM vignette
ggPlotMultiDensities | Plot multiple density distributions
joinOutputs | Joins outputs from multiple invocations of the function 'dipalm'.
main | Runs the full DiPALM pipeline with replicate permutation in parallel.
make_TCs | Break a data matrix into time courses separated by treatment and replicate.
msub | Regex substitution applied to a vector or list.
open_log | Open a log
PlotTCs | Plot multiple time-course expression patterns for one gene
PlotTCsRibbon | Plot multiple averaged time-course expression patterns for a group of genes
re_esc | Format a string as a regular expression literal.
sampleReplicates | Samples replicates from a dataset without replacement.
smallTestData | Small test data for the DiPALM pipeline.
testData | Test Data: Data for function testing