NEWS

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swissknife 0.42

• Expose nbins argument (to sampleControlElements) in normGenesetExpression
• Allow single-gene sets in normGenesetExpression

swissknife 0.41

• Add weightedMeanByID to aggregate values by an ID

swissknife 0.40

• Add loadExampleData for loading of data sets used in teaching

swissknife 0.39

• Change the file name of the utility function test file, wrap tests in test_that

swissknife 0.38

• Add plotTitle argument to plotGeneRegion

swissknife 0.37

• Add ellipsis to plotGeneRegion to allow additional arguments to plotTracks

swissknife 0.36

• Add .assertPackagesAvailable utility function and unit test to templates
• Update internally used .assertPackagesAvailable to be identical to the ones in templates

swissknife 0.35

• Expand capabilities of utility functions, add unit tests
• fix bowtie executable location logic for windows

swissknife 0.34

• Bug fix - expand documentation in utility functions.

swissknife 0.33

• Add addUtilsFunctions to include utility functions in other packages

swissknife 0.32

• Add getInsertSizeDistFromBam to tabulate insert sizes from paired-end alignments in bam files

swissknife 0.31

• Fix readSampleTsvs so that provided patterns must match from the beginning of the filename

swissknife 0.30

• Speed-up package load time by moving rarely used Depends to Suggests

swissknife 0.29

• Refactor getGenomicTiles, adding a new annotateRegions that accepts any GRanges as input

swissknife 0.28

• Truncate chromosome names after first whitespace in getGenomicTiles when checking consistency

swissknife 0.27

• Add getGenomicTiles to obtain annotated regions tiling a given genome

swissknife 0.26

• speed-up getMappableRegions by dumping k-mers in C++

swissknife 0.25

• fix getMappableRegions to work for fully mappable chromosomes

swissknife 0.24

• Add getMappableRegions to obtain mappable regions in a genome

swissknife 0.23

• Add specificityScore to calculate (tissue) specificity of gene expression

swissknife 0.22

• ignore NA values in normGenesetExpression

swissknife 0.21

• Add labelCells to label cells using sets of marker genes
• Add normGenesetExpression to calculate normalized expression of a set of genes

swissknife 0.20

• set seed in unit test for sampleControlElements

swissknife 0.19

• fix coloring bugin in plotGeneRegion

swissknife 0.18

• setup github actions and remove travis

swissknife 0.17

• Add R/selVarGenes.R to select variable genes in a single cell RNA-seq experiment
• configured travis/github to automatically run pkgdown::deploy_site_github()

swissknife 0.16

• Show features that overlap selected regions only with their introns in plotGeneRegion

swissknife 0.15

• Allow specification of colors for coverage tracks in plotGeneRegion

swissknife 0.14

• Allow coloring features by strand in plotGeneRegion

swissknife 0.13

• Add parsePkgVersions
• Add plotGeneRegion

swissknife 0.12

• Add col2hex

swissknife 0.11

• Add ypixels, pointsize argument to plotBitScatter

swissknife 0.9

• Add R/valueToColor.R

swissknife 0.8

• plotBitScatter(x, y = NULL) now also works for x being a two-column matrix

swissknife 0.7

• add functions to calculate and plot phasograms, e.g. to measure nucleosome repeat length in MNase data (R/phasograms.R, src/phasograms.cpp)

swissknife 0.6

• added tests for sampleControlElements() to cover all code (coverage gaps detected with covr::zero_coverage(covr::package_coverage()))

swissknife 0.5

• sampleControlElements() now catches cases with too few control elements to match the target distribution

swissknife 0.4

• sampleControlElements(x = list(), ...) now works correctly

swissknife 0.3

• Add R/readSampleTsvs.R:readSampleTsvs()

swissknife 0.2

• Add R/plotting.R:plotBitScatter()

swissknife 0.1

• Initial version
• add R/misc.R:sampleControlElements()