Reference

All functions

DEqual()

Differential expression quality (DEqual) plot

degradation_tstats

Degradation time t-statistics

getDegTx()

Obtain expression matrix for degraded transcripts

getPCs()

PCs from transcripts

get_qsvs()

Generate matrix of qsvs

k_qsvs()

Apply num.sv algorithm to determine the number of pcs to be included

normalize_tx_names()

Remove version number from Gencode/Ensembl transcript names

qSVA()

A wrapper function used to perform qSVA in one step.

rse_tx

Example of RSE object with RNA-seq transcript quantification data

select_transcripts()

Select transcripts associated with degradation

transcripts

Transcripts for Degradation Models

which_tx_names()

Check validity of transcript vectors and return a vector matching indexes in tx1