Changelog

Source: NEWS.md

swissknife 0.43

  • Update utils templates to use cli
  • Add .message utility function to utils template

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 0.10 / 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()