All functions

annotable arrange as_tibble filter gene2entrez gene2symbol mutate tx2gene

S4 generics

annotable gene2entrez gene2symbol tx2gene

Ensembl annotations

assignAsNewEnv

Assign multiple objects to a new environment

basejump

toStringUnique toStringSortUnique summarizeRows

Collapse utilities

detectOrganism

Detect the organism from the genome build name

comp revcomp

DNA sequence utilites

fixNA

Fix character strings missing NA

geomean

Geometric mean

grepString

grep string generator

kables

Create tables in LaTeX, HTML, Markdown and reStructuredText

loadData loadRemote

Data loading utilities

fc2lr lr2fc

Interconvert log ratio and fold change values

mdHeader

Markdown header

mdList

Markdown list

camel dotted snake titleCase firstCase

Make syntactically valid names

packageSE

Package into a SummarizedExperiment

pct

Convert numeric to percentage

createProjectDirs detectHPC packageProject renderProject

Project management utilities

readDataRaw

Read CSV files inside data-raw directory

readFileByExtension

Read file by extension

readYAML

Read YAML file

removeNA

Remove rows and columns containing only NA values

saveData saveDataRaw assignAndSaveData

Save data objects

sortUnique

Quickly perform sort unique on a vector

arrange as_tibble content expand filter first intersect mutate rename setdiff setequal union

tidyverse S4 methods

transmit

Transmit (download) files from a remote server

wash

Wash a data frame

writeCounts

Write counts