NEWS
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
swissknife 0.11
- Add ypixels, pointsize argument to plotBitScatter
swissknife 0.9
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()