DSS-package |
Dispersion shrinkage for sequencing data |
callDML |
Function to detect differntially methylated loci (DML) from bisulfite sequencing (BS-seq) data. |
callDMR |
Function to detect differntially methylated regions (DMR) from bisulfite sequencing (BS-seq) data. |
design |
Experimental design for the example RRBS dataset |
dispersion |
Acessor functions for the 'dispersion' slot in a SeqCountData object. |
dispersion-method |
Acessor functions for the 'dispersion' slot in a SeqCountData object. |
dispersion<- |
Acessor functions for the 'dispersion' slot in a SeqCountData object. |
dispersion<--method |
Acessor functions for the 'dispersion' slot in a SeqCountData object. |
DMLfit.multiFactor |
Fit a linear model for BS-seq data from general experimental design |
DMLtest |
Function to perform statistical test of differntially methylated loci (DML) for two group comparisons of bisulfite sequencing (BS-seq) data. |
DMLtest.multiFactor |
Perform statistical test for BS-seq data from general experimental design |
DSS |
Dispersion shrinkage for sequencing data |
DSS.DE |
Perform RNA-seq differential expression analysis in two-group comparison |
estDispersion |
Estimate and shrink tag-specific dipsersions |
estDispersion-method |
Estimate and shrink tag-specific dipsersions |
estNormFactors |
Estimate normalization factors |
estNormFactors-method |
Estimate normalization factors |
makeBSseqData |
Create an object of BSseq class from several data frames. |
newSeqCountSet |
Class '"SeqCountSet"' - container for count data from sequencing experiment |
normalizationFactor |
Accessor functions for the 'normalizationFactor' slot in a SeqCountData object. |
normalizationFactor-method |
Accessor functions for the 'normalizationFactor' slot in a SeqCountData object. |
normalizationFactor<- |
Accessor functions for the 'normalizationFactor' slot in a SeqCountData object. |
normalizationFactor<--method |
Accessor functions for the 'normalizationFactor' slot in a SeqCountData object. |
RRBS |
An example dataset for multiple factor design |
SeqCountSet |
Class '"SeqCountSet"' - container for count data from sequencing experiment |
SeqCountSet-class |
Class '"SeqCountSet"' - container for count data from sequencing experiment |
seqData |
A simulated 'SeqCountData' object. |
showOneDMR |
Visualze the count data for one DMR |
waldTest |
Perform gene-wise Wald test for two group comparisons for sequencing count data. |
waldTest-method |
Perform gene-wise Wald test for two group comparisons for sequencing count data. |