Changes in version 0.44 - Add addLintrConfig to add a lintr config file to a package Changes in version 0.43 - Update utils templates to use cli - Add .message utility function to utils template Changes in version 0.42 - Expose nbins argument (to sampleControlElements) in normGenesetExpression - Allow single-gene sets in normGenesetExpression Changes in version 0.41 - Add weightedMeanByID to aggregate values by an ID Changes in version 0.40 - Add loadExampleData for loading of data sets used in teaching Changes in version 0.39 - Change the file name of the utility function test file, wrap tests in test_that Changes in version 0.38 - Add plotTitle argument to plotGeneRegion Changes in version 0.37 - Add ellipsis to plotGeneRegion to allow additional arguments to plotTracks Changes in version 0.36 - Add .assertPackagesAvailable utility function and unit test to templates - Update internally used .assertPackagesAvailable to be identical to the ones in templates Changes in version 0.35 - Expand capabilities of utility functions, add unit tests - fix bowtie executable location logic for windows Changes in version 0.34 - Bug fix - expand documentation in utility functions. Changes in version 0.33 - Add addUtilsFunctions to include utility functions in other packages Changes in version 0.32 - Add getInsertSizeDistFromBam to tabulate insert sizes from paired-end alignments in bam files Changes in version 0.31 - Fix readSampleTsvs so that provided patterns must match from the beginning of the filename Changes in version 0.30 - Speed-up package load time by moving rarely used Depends to Suggests Changes in version 0.29 - Refactor getGenomicTiles, adding a new annotateRegions that accepts any GRanges as input Changes in version 0.28 - Truncate chromosome names after first whitespace in getGenomicTiles when checking consistency Changes in version 0.27 - Add getGenomicTiles to obtain annotated regions tiling a given genome Changes in version 0.26 - speed-up getMappableRegions by dumping k-mers in C++ Changes in version 0.25 - fix getMappableRegions to work for fully mappable chromosomes Changes in version 0.24 - Add getMappableRegions to obtain mappable regions in a genome Changes in version 0.23 - Add specificityScore to calculate (tissue) specificity of gene expression Changes in version 0.22 - ignore NA values in normGenesetExpression Changes in version 0.21 - Add labelCells to label cells using sets of marker genes - Add normGenesetExpression to calculate normalized expression of a set of genes Changes in version 0.20 - set seed in unit test for sampleControlElements Changes in version 0.19 - fix coloring bugin in plotGeneRegion Changes in version 0.18 - setup github actions and remove travis Changes in version 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() Changes in version 0.16 - Show features that overlap selected regions only with their introns in plotGeneRegion Changes in version 0.15 - Allow specification of colors for coverage tracks in plotGeneRegion Changes in version 0.14 - Allow coloring features by strand in plotGeneRegion Changes in version 0.13 - Add parsePkgVersions - Add plotGeneRegion Changes in version 0.12 - Add col2hex Changes in version 0.11 - Add ypixels, pointsize argument to plotBitScatter Changes in version 0.9 - Add R/valueToColor.R Changes in version 0.8 - plotBitScatter(x, y = NULL) now also works for x being a two-column matrix Changes in version 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) Changes in version 0.6 - added tests for sampleControlElements() to cover all code (coverage gaps detected with covr::zero_coverage(covr::package_coverage())) Changes in version 0.5 - sampleControlElements() now catches cases with too few control elements to match the target distribution Changes in version 0.4 - sampleControlElements(x = list(), ...) now works correctly Changes in version 0.3 - Add R/readSampleTsvs.R:readSampleTsvs() Changes in version 0.2 - Add R/plotting.R:plotBitScatter() Changes in version 0.1 - Initial version - add R/misc.R:sampleControlElements()