Adjust transcript abundance for unwanted variation
Aggregates multiple counts from the same samples (e.g., from isoforms), concatenates other character columns, and averages other numeric columns
Efficiently bind multiple data frames by row and column
Check whether there are duplicated genes/transcripts
Get clusters of elements (e.g., samples or transcripts)
Get DESCRIPTION from gene SYMBOL for Human and Mouse
Add transcript symbol column from ensembl id for human and mouse data
Fill transcript abundance if missing from sample-transcript pairs
Produces the bibliography list of your workflow
impute transcript abundance if missing from sample-transcript pairs
Dimension reduction of the transcript abundance data
Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) abundances are correlated
Rotate two dimensions (e.g., principal components) of an arbitrary angle
Perform differential transcription testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2
Add differential tissue composition information to a tbl
analyse gene over-representation with GSEA
Test of stratification of biological replicates based on tissue composition, one cell-type at the time, using Kaplan-meier curves.
Creates an annotated 'tidybulk' tibble from a 'tbl' or 'SummarizedExperiment' object
Creates a 'tt' object from a list of file names of BAM/SAM
Needed for tests tximeta_summarizeToGene_object, It is SummarizedExperiment from tximeta