Package: erccdashboard 1.41.0

Sarah Munro

erccdashboard: Assess Differential Gene Expression Experiments with ERCC Controls

Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures.

Authors:Sarah Munro, Steve Lund

# Install 'erccdashboard' in R:

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

Datasets:

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

Last updated 2 months agofrom:e3aeeef274. Checks:OK: 1 NOTE: 6. Indexed: yes.

Sarah Munro, Steve Lund

Last update: 2024-10-26
Started: 2024-10-26

Help page	Topics
Annotate signal-abundance and ratio-abundance plots with LODR	annotLODR
Produce signal-abundance plot to evaluate dynamic range	dynRangePlot
ERCC data	ERCC
ERCCDef dataframe	ERCCDef
ERCCMix1and2 dataframe	ERCCMix1and2
Produce Receiver Operator Characteristic (ROC) Curves and AUC statistics	erccROC
Estimate the mRNA fraction differences for the pair of samples using replicate data	est_r_m
Estimate Limit of Detection of Ratios (LODR)	estLODR
Prepare differential expression testing results for spike-in analysis	geneExprTest
Initialize the exDat list	initDat
Generate MA plots with or without annotation using LODR estimates	maSignal
Rat toxicogenomics count data	MET.CTL.countDat
Rat toxicogenomics total read data	MET.CTL.totalReads
Run default erccdashboard analysis of ERCC control ratio mixtures	runDashboard
Save erccdashboard plots to a pdf file	saveERCCPlots
Example data from SEQC project for erccdashboard analysis	SEQC.Example
UHRR and HBRR Illumina BeadArray data	UHRR.HBRR.arrayDat
UHRR and HBRR RNA-Seq Illumina count data	UHRR.HBRR.countDat
UHRR and HBRR sample total read data	UHRR.HBRR.totalReads