| 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 |