All functions

aggregateFeatures

Aggregate Features

aggregateReplicates

Aggregate Replicates

annotable

Ensembl Annotations

assertAllAreNonExisting

Assert All Variables Are Non-Existing

assertFormalAnnotationCol

Assert Formal Annotation Column

assertFormalCompress

Assert Formal Compression

assertFormalGene2symbol

Assert Formal Gene to Symbol Mappings

assertHasRownames hasRownames

Assert Has Rownames

assertIsAHeaderLevel

Assert Is a Header Level

assertIsAnIntegerOrNULL

Assert Is an Integer or NULL

assertIsAnnotable

Assert Is Ensembl Annotations Data Frame

assertIsANumberOrNULL

Assert Is a Number or NULL

assertIsAStringOrNULL

Assert Is a String or NULL

assertIsCharacterOrNULL

Assert Is Character Vector or NULL

assertIsColorScaleContinuousOrNULL

Assert Is Color Palette Scale Continuous or NULL

assertIsColorScaleDiscreteOrNULL

Assert Is Color Palette Scale Discrete or NULL

assertIsDataFrameOrNULL

Assert Is Data Frame or NULL

assertIsFillScaleContinuousOrNULL

Assert Is Fill Palette Scale Continuous or NULL

assertIsFillScaleDiscreteOrNULL

Assert Is Fill Palette Scale Discrete or NULL

assertIsGene2symbol

Assert Is Gene to Symbol Mapping Data Frame

assertIsHexColorFunctionOrNULL

Assert Is Hex Color Function or NULL

assertIsAnImplicitInteger assertIsAnImplicitIntegerOrNULL assertIsImplicitInteger assertIsImplicitIntegerOrNULL isImplicitInteger

Assert Is Implicit Integer

assertIsTx2gene

Check Transcript to Gene Mapping Data

assignAndSaveData

Assign and Save Data

basejump-package

basejump

camel upperCamel

Camel Case

collapseToString

Collapse to String

convertGenesToSymbols

Convert Ensembl Identifier to Gene Symbol

convertTranscriptsToGenes

Convert Ensembl Transcripts to Genes

detectHPC

Detect HPC Environment

detectOrganism

Detect Organism

dots

Extract Dots from Function

dotted

Dotted Case

dynamicPlotlist

Dynamic Plotlist

fixNA

Fix Character Strings Missing NA

gene2symbol

Ensembl Gene to Symbol Mappings

gene2symbolFromGFF gene2symbolFromGTF

Define Gene to Symbol Mappings from GFF/GTF File

geometricMean geomean

Geometric Mean

grepString

grep String Generator

initializeDirectory

Initialize Directory

kables

Create Tables in LaTeX, HTML, Markdown and reStructuredText

loadData

Load Local Data

loadDataAsName

Load Data File as Name

loadRemoteData

Load Remote Data

localOrRemoteFile

Dynamically Handle a Local or Remote File Path

foldChangeToLogRatio logRatioToFoldChange

Interconvert Log Ratio and Fold Change Values

markdownHeader mdHeader

Markdown Header

markdownList mdList

Markdown List

markdownPlotlist mdPlotlist

Markdown Plotlist

microplate

Microtiter Plate Well Identifiers

midnightTheme theme_midnight

Midnight Theme

multiassignAsNewEnvir

Assign Multiple Objects as a New Environment

plotHeatmap

Plot Heatmap

plotQuantileHeatmap

Plot Heatmap with Quantile Breaks

readFileByExtension

Read File by Extension

readGFF readGTF

Read GFF/GTF Annotations

readYAML

Read YAML File

removeNA

Remove Rows and Columns Containing Only NA Values

sanitizeAnnotable

Sanitize Ensembl Annotations

sanitizeColData

Sanitize Column Data Frame

saveData

Save Data

snake

Snake Case

sortUnique

Quickly Perform Sort Unique on a Vector

stripTranscriptVersions

Strip Transcript Versions

toStringUnique

Convert to a Unique Character String

transmit

Transmit Files from a Remote FTP Server

tx2gene

Transcript to Gene Mappings

tx2geneFromGFF tx2geneFromGTF

Define Transcript to Gene Mappings from GFF/GTF File

writeCounts

Write Counts