basejump 0.1.0 (2017-10-23)

  • Bump version to match bcbioRNASeq package.
  • Improved unit testing coverage of prepareSummarizedExperiment.
  • Added quiet mode support to functions that output messages, where applicable.
  • Consolidated roxygen2 function imports to basejump-package.R file.
  • Deprecated sampleDirs generic.
  • Improved organism detection in detectOrganism and added support for chicken genome.
  • Clarified warning messages in prepareSummarizedExperiment to make sample loading with loadRNASeq and loadSingleCell in the bcbio packages less confusing.
  • Improved NULL returns in readDataVersions, readLogFile, and readProgramVersions utility functions.
  • Fixed export of *GTF alias functions to simply wrap the *GFF functions with S4 methods support.
  • Improved lane split technical replicate handling in readSampleMetadataFile.
  • Improved camel syntax for both lax and strict modes. Added upperCamel function.
  • Switched str_ to base grep and gsub in internal functions.

basejump 0.1.1 (2017-11-11)

  • Added overwrite support for saveData. Now will skip on existing files when overwrite = FALSE.
  • Bug fix for readDataVersions, which shouldn’t have the column types defined, using col_types = "ccT".
  • Improved key value pair method for loadDataAsName. Now rather than using a named character vector for the mappings argument, the user can simply pass the key value pairs in as dots. For example, newName1 = "oldName1", newName2 = "oldName2". The legacy mappings method will still work, as long as the dots argument is a length of 1.
  • Ensembl release version now defaults to NULL instead of current for annotable, gene2symbol, symbol2gene and tx2gene functions.
  • Allow rowData to be left unset in prepareSummarizedExperiment. This is useful for setting up objects that don’t contain gene annotations.
  • Removed sample selection by pattern matching (pattern, patternCol arguments) in readSampleMetadata. This feature wasn’t fully baked and doesn’t offer enough functionality to the user.

basejump 0.1.2 (2017-11-30)

  • Added bcbio plotQC generic.
  • Added back toStringUnique code, which is still in use in the wormbase package.
  • Added deprecations for summarizeRows (now collapseToString) and wash functions.
  • Updated installation method to include manual installation of ensembldb. Otherwise, basejump installation fails due to GenomeInfoDb and GenomeInfoDbData not getting installed completely.
  • Now suggesting that the user installs suggested packages in the README.
  • Updated PANTHER annotation scripts.
  • Bug fix for detectOrganism. Now allowing NULL return for unsupported organism, with a warning.

basejump 0.1.3 (2017-12-01)

  • loadData and loadDataAsName now default to replace = TRUE. If an object with the same name exists in the destination environment, then a warning is generated.
  • collapseToString only attempts to dynamically return the original object class on objects that aren’t class data.frame. I updated this code to behave more nicely with grouped tibbles (grouped_df), which are a virtual class of data.frame and therefore can’t be coerced using as(object, "grouped_df").
  • DNA sequence utility functions comp and revcomp now return NULL for integers and numerics.
  • For prepareSummarizedExperiment, added support for dropping NULL objects in assays list. This is useful for handling output from bcbioRNASeq when transformLimit is reached. In this case, the rlog and vst matrices aren’t generated and set NULL in the assays list. Using Filter(Negate(is.null), assays) we can drop these NULL objects and prevent a downstream dimension mismatch in the SummarizedExperiment::SummarizedExperiment call.
  • Improved support for multiplexed files in readSampleMetadataFile. This now checks for a sequence column containing ACGT nucleotides. When those are detected, the revcomp column is generated. Otherwise this step is skipped. This is useful for handling multiplexed sample metadata from 10X Genomics Cell Ranger single-cell RNA-seq samples.
  • Updated annotable function to include nested Entrez identifiers in the entrez column. This is useful for downstream functional analysis.

basejump 0.1.4 (2017-12-04)

  • Added midnightTheme ggplot2 theme. Originally this was defined as darkTheme in the bcbioSingleCell package, but can be useful for other plots and has been moved here for general bioinformatics usage. The theme now uses ggplot2::theme_minimal as the base, with some color tweaks, namely dark gray axes without white axis lines.
  • Improve NAMESPACE imports to include stats::formula and utils::capture.output.

basejump 0.1.5 (2017-12-05)

  • Added checkAnnotable, checkGene2symbol, checkTx2gene, and sanitizeAnnotable utility functions that will be used in the bcbio R packages.

basejump 0.1.6 (2017-12-06)

  • Moved microplate code from the wormbase package here, since it’s of general interest.

basejump 0.1.7 (2017-12-11)

  • Renamed fc2lr to foldChangeToLogRatio and lr2fc and logRatioToFoldChange.
  • Moved plotDot and plotViolin generics here from bcbioSingleCell.
  • Added internal GRCh37 gene annotations.

basejump 0.1.8 (2017-12-14)

  • Improved matrix and dgCMatrix method support in aggregateReplicates and aggregateFeatures functions. Both of these functions now use a consistent groupings parameter, which uses a named factor to define the mappings of either samples (columns) for aggregateReplicates or genes/transcripts (rows) for aggregateFeatures.
  • Update for makeNames sanitization functions. Now they will work on names(x) for vectors by default.
  • Improved detectOrganism to match against “H. sapiens”, etc.
  • Added internal GRCh37 transcript to gene mapping.
  • Improved organism matching to detect “Homo_sapiens” and “H. sapiens”.
  • Factors are now supported in the makeNames utilities: camel, dotted, snake, and upperCamel.
  • Improved handling of NA values from LibreOffice and Microsoft Excel output in readFileByExtension. This function now sets "", NA, and #N/A strings as NA correctly.

basejump 0.1.9 (2017-12-18)

  • Added plotHeatmap functionality.
  • Migrated tpm generic from bcbioRNASeq, for future use in bcbioSingleCell.
  • Added matrix method support for plotHeatmap.
  • Added matrix method support for plotQuantileHeatmap, which works similarly as plotHeatmap.

basejump 0.1.10 (2017-12-20)

  • Bug fix for multiplexed sample input into readSampleMetadataFile. We were detecting the presence of index column but should instead check against sequence column.
  • Added dynamicPlotlist and mdPlotlist plotting utilities.
  • Added uniqueSymbols parameter to annotable function.