Reference

calcPhasogram()

Calculate phasograms (same strand alignment distances).

estimateNRL()

Estimate the nucleosome repeat length (NRL) from a phasogram.

plotPhasogram()

Plot annotated phasogram.

calcAndCountDist()

Count frequency of differences between values in integer vectors.

selVarGenes()

Select Variable Genes in Single Cell RNA-seq

plotSelVarGenes()

Plot Selected Variable Genes

normGenesetExpression()

Calculate normalized expression of a gene set

labelCells()

Assign labels to cells using known marker genes

specificityScore()

Calculate gene-expression specificity scores.

plotBitScatter()

Create a bitmap-rendered plot.

valueToColor()

Map numerical values to colors.

col2hex()

Get hex color

plotGeneRegion()

Plot gene region

readSampleTsvs()

Read sample tsv files from seqdata storage

sampleControlElements()

Sample control elements that match a target distribution.

parsePkgVersions()

Parse R and R package versions from session informations

prepareGTF()

Prepare GTF file for use with plotGeneRegion

annotateRegions()

Annotate regions.

getInsertSizeDistFromBam()

Tabulate insert sizes from paired-end alignments in bam files.

getMappableRegions()

Get mappable regions of a genome.

getGenomicTiles()

Get regions tiling a genome.

addUtilsFunctions()

Copy utility functions to package

loadExampleData()

Access example data

weightedMeanByID()

Aggregate different rows assigned to the same ID by calculating a weighted mean

swissknife swissknife-package

swissknife - handy code shared in the FMI CompBio group