Count model based differential expression and normalization on GeoMx RNA data

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Documentation for package ‘GeoDiff’ version 1.12.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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