# Count model based differential expression and normalization on GeoMx RNA data

## Documentation for package ‘GeoDiff’ version 1.4.0

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

## Help Pages

aggreprobe | Generate aggregated counts of probes for the same target
aggreprobe-method | Generate aggregated counts of probes for the same target
BGScoreTest | Testing for features above the background
BGScoreTest-method | Testing for features above the background
BGScoreTest_sp | Testing for features above the background, multiple slides case
BGScoreTest_sp-method | Testing for features above the background, multiple slides case
coefNBth | Generate list of Wald test inference results on model coefficients
coefNBth-method | Generate list of Wald test inference results on model coefficients
contrastNBth | Generate list of Wald test inference results on user specified contrasts
contrastNBth-method | Generate list of Wald test inference results on user specified contrasts
demoData | A demo dataset for GeoMx Cancer Transcriptome Atlas (CTA) panel
DENBth | Generate DE table using the inference list generated by coefNBth or contrastNBth
DENBth-method | Generate DE table using the inference list generated by coefNBth or contrastNBth
diagPoisBG | Perform diagnosis on Poisson background model
diagPoisBG-method | Perform diagnosis on Poisson background model
fitNBth | Negative Binomial threshold model
fitNBth-method | Negative Binomial threshold model
fitNBthDE | Negative Binomial threshold model for differential expression analysis
fitNBthDE-method | Negative Binomial threshold model for differential expression analysis
fitNBthmDE | Negative Binomial threshold mixed model for differential expression analysis
fitNBthmDE-method | Negative Binomial threshold mixed model for differential expression analysis
fitPoisBG | Estimate Poisson background model for either single slide or multiple slides
fitPoisBG-method | Estimate Poisson background model for either single slide or multiple slides
fitPoisBG_sp | Estimate Poisson background model for multiple slides
fitPoisBG_sp-method | Estimate Poisson background model for multiple slides
fitPoisthNorm | Poisson threshold model based normalization-log2 transformation for single slide or for multiple slides
fitPoisthNorm-method | Poisson threshold model based normalization-log2 transformation for single slide or for multiple slides
fitPoisthNorm_sp | Poisson threshold model based normalization-log2 transformation for multiple slides
fitPoisthNorm_sp-method | Poisson threshold model based normalization-log2 transformation for multiple slides
kidney | A demo dataset for GeoMx Human Whole Transcriptome Atlas (WTA) panel
NBthDEmod2 | A demo example output list returned by function fitNBthDE
NBthmDEmod2 | A demo example output list returned by function fitNBthmDE
NBthmDEmod2slope | A demo example output list returned by function fitNBthmDE
QuanRange | Compute Quantile Range
QuanRange-method | Compute Quantile Range