Count model based differential expression and normalization on GeoMx RNA data


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Documentation for package ‘GeoDiff’ version 1.4.0

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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