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Version 0.11

basejump 0.11.0 (2019-07-22)

Start of new release series. Version bump reflects changes in dependency packages. See the acidtest, bioverbs, freerange, syntactic, and transformer release notes for more details.

basejump 0.11.1 (2019-07-24)

Minor changes:

  • Added back deprecated assert checks that are required for bcbioRNASeq v0.2 release series.

basejump 0.11.2 (2019-07-29)

Minor changes:

  • Reexporting new functions in syntactic: makeLabel, makeTitle, makeWords.
  • Updated documentation to include modification timestamp.

basejump 0.11.3 (2019-07-30)

100th release!

Minor changes:

  • mapCellsToSamples: Relaxed grep matching on cells input to support legacy bcbioSingleCell objects. This change was needed to improve updateObject method in the upcoming bcbioSingleCell update.

basejump 0.11.4 (2019-08-07)

Major changes:

  • makeSampleData: Switched to S4 method that works on data.frame and DataFrame class objects. Enforcing lower camel case for column names.
  • makeSummarizedExperiment and makeSingleCellExperiment: Switched to S4 method approach that currently requires SimpleList input for assays. Previously, we allowed list input for assays, but we’re tightening this up to simply the package code base and improve consistency.
  • aggregate methods now consistently return the primary assay named as counts. This follows the recommended conventions defined in SingleCellExperiment. Aggregation functions will now intentionally fail for SummarizedExperiment objects that don’t contain an assay named counts.

Minor changes:

  • Improved documentation consistency by offloading params.Rd file to new acidroxygen package. This will be linked in the other Acid Genomics packages.
  • Updated unit tests to follow new package conventions (see above changes).

basejump 0.11.5 (2019-08-11)

New functions:

  • calculateMetrics: Migrated code here from bcbioSingleCell. Improved method to support DelayedArray class for large matrices.

Minor changes:

  • Improved code coverage and adjusted unit tests for breaking changes seen due to new covr update.

basejump 0.11.6 (2019-08-12)

Minor changes:

  • Updated goalie dependency.
  • Tightened up appendToBody and methodFormals calls to have better backward compatibility with R 3.5.
  • calculateMetrics: Bug fix for getting rowData via mcols without use.names = TRUE. This improves Bioconductor backward compatibility. Also updated internal code to call hasMetrics from goalie.
  • Made separatorBar defunct. Use separator function instead.

basejump 0.11.7 (2019-08-13)

Minor changes:

  • filterCells: Improved downstream handling of nCells argument. Ensure double filtering is still allowed.

basejump 0.11.8 (2019-08-19)

New functions:

  • Migrated readSampleData and readTx2Gene from bcbioBase.
  • Reworked readSampleData internal code, but still supporting bcbio pipeline conventions (i.e. “description” column for samples) as the default. I’ve reworked this approach so we can also call readSampleData inside the Chromium package (for 10X Genomics single-cell RNA-seq data) without having to depend on the bcbio R packages.
  • Reexporting new dplyr-like methods that support S4 DataFrame: inner_join, left_join, right_join, full_join, anti_join; mutate_all, mutate_at, mutate_if; select_all, select_at, select_if.

Major changes:

  • Removed dplyr and magrittr dependencies in internal code, where applicable.
  • aggregateCols: Sped up return by calling SingleCellExperiment rather than makeSingleCellExperiment. Note that this now doesn’t return session information in the object.
  • cell2sample: Renamed return from tibble to tbl_df, for consistency.
  • Made some previous deprecated functions still used in bcbioRNASeq v0.2 release series (which has now been updated to v0.3) defunct. This applies primarily to assert* functions that have been reworked using a goalie approach.
  • estimateSizeFactors: Removed option to calculate “deseq2-median-ratio” using DESeq2. We may revisit this idea in a future release.
  • makeSampleData: Improved internal code for DataFrame method.

Minor changes:

  • Updated basejump dependencies, in preparation for bioconda release update supporting bcbioRNASeq.
  • Now importing AnnotationDbi, BiocParallel, Biostrings, and biomaRt.
  • Safe to import select from AnnotationDbi, now that we’re no longer depending on dplyr.
  • Switched to using droplevels instead of relevel on S4 objects internally, where applicable. This is better supported by S4Vectors package.
  • Simplified reexport documentation for S4 functions and methods.

basejump 0.11.9 (2019-08-21)

Minor changes:

  • meltCounts: Added initial method support for SingleCellExperiment. Currently requires deparsing of the count matrix to call reshape2::melt. Returns columns with S4 run-length encoding (Rle) applied.
  • mapGenes: Converted warning to message when strict = FALSE.

basejump 0.11.10 (2019-08-22)

Minor changes:

  • makeSummarizedExperiment: Now automatically handles non-Ensembl gene symbols present in assays that aren’t defined in rowRanges. This applies primarily to 10X Cell Ranger v3 output, which includes some non-Ensembl gene symbols: CD11b, CD4, CD8a, HLA-DR, IgG1, PD-1, etc. The function still intentionally errors on unannotated Ensembl features, which often indicates an accidental release version mismatch.
  • Updated dependency versions.

basejump 0.11.11 (2019-08-27)

Updated R dependency to 3.6.

New functions:

  • melt: Added S4 methods for melting data into long format. Provides support for matrix, Matrix, DataFrame, SummarizedExperiment, and SingleCellExperiment currently.
  • nonzeroRowsAndCols: Quickly remove non-zero rows and columns from a matrix or SummarizedExperiment.

Major changes:

  • Migrated EggNOG and PANTHER S4 classes to separate packages.

Minor changes:

  • calculateMetrics: Now calls nonzeroRowsAndCols internally first when prefilter = FALSE, speeding up calculations significantly for very large SingleCellExperiment objects. This was added to improve loading of example unfiltered 10X Genomics Chromium data.

Deprecations:

  • Deprecated readSampleData and readTx2Gene in favor of importSampleData and importTx2Gene, respectively.

basejump 0.11.12 (2019-09-03)

Minor changes:

  • melt: Added method support for contingency table class.
  • Removed set_* reexports from magrittr packages.

basejump 0.11.13 (2019-09-06)

Major changes:

  • autopadZeros: Added improved support for detection and automatic handling of zeros in need of padding on the left side of a character vector. This addition is necessary for handling of Genewiz processed FASTQ file names.
  • makeTx2Gene functions now support ignoreTxVersion argument, similar to conventions defined in tximport package.

Minor changes:

  • importSampleData: Updated to tentatively support a general pipeline via the “none” argument. In this case, only a sampleID column is required in metadata. This is been developed in conjunction with my new Genewiz to kallisto Nextflow processing pipeline being implemented at CPI.

basejump 0.11.14 (2019-09-09)

Minor changes:

  • mcolnames: Moved S4 methods previously defined in syntactic here.
  • Improved website documentation.

basejump 0.11.15 (2019-09-16)

Major changes:

  • melt: Updated min and minMethod defaults for matrix method. The min argument now defaults to -Inf, and the minMethod now defaults to "absolute", instead of "perRow", since this behavior is more intuitive to the user.

Minor changes:

  • nonzeroRowsAndCols: Added assay argument, switching from internal counts usage, to make the SummarizedExperiment method more flexible.

basejump 0.11.16 (2019-09-25)

Minor changes:

  • Migrated S4 methods from syntactic that work on Bioconductor classes here. This keeps the syntactic package very light weight and focused only on character string sanitization.

basejump 0.11.17 (2019-10-09)

Minor changes:

  • makeSampleData: Made function slightly more flexible. Now allowing automatic rowname coercion from columns (“sampleID”, “rowname”, “rn”), similar to approach employed by data.table and tibble packages.
  • Now exporting stripGeneVersions alias, which uses the same code internally as stripTranscriptVersions.

Disabled methods:

  • Disabled DelayedArray class methods for calculateMetrics, estimateSizeFactors, and nonzeroRowsAndCols until is_pristine bug in DelayedArray v0.11.8 is fixed on Bioconductor Devel (3.10). This is causing unit tests to fail otherwise. See related issue

basejump 0.11.18 (2019-10-13)

Minor changes:

  • importSampleData: Pipeline now defaulting to “none” instead of “bcbio”, since this flag is now properly hard coded in bcbio R packages. Added new Constellation (CPI) pipeline option.
  • makeSampleData: Now checks for all NA columns and rows, similar to approach in importSampleData. This helps improve return consistency. Automatic rowname setting has been tweaked a bit to no longer attempt to remove original ID column.

basejump 0.11.19 (2019-10-23)

New functions:

  • Genome version detection: ensemblVersion, gencodeVersion, refseqVersion, flybaseVersion, wormbaseVersion. Similar shell variants are available in the koopa package.

Minor changes:

  • Moved some low-level functions to new acidbase package. Updated NAMESPACE and reexports to reflect these changes.

basejump 0.11.20 (2019-10-24)

New reexports:

  • Reexporting metadata2 and metadata2<- functions from transformer. These will be used internally in the pending DESeqAnalysis update.

basejump 0.11.21 (2019-11-07)

Major changes:

  • Updated Bioconductor dependencies to require new 3.10 release.

Bug fixes:

  • filterCells requires an internal decode step to handle Rle evaluation, which worked previously in Bioconductor 3.9 release.
  • Updated unit tests to reflect SingleCellExperiment example object resave in acidtest 0.2.7 update, which changed the numbers.

basejump 0.11.22 (2019-11-11)

New functions:

  • correlation: Added S4 method support that mimics base cor methods, but is more flexible, supporting additional arguments via ... in generic. This way we can provide intelligent and quick correlation calculations for nested assays inside a SummarizedExperiment and for DESeqResults (see DESeqAnalysis package).

basejump 0.11.23 (2019-11-19)

Minor changes:

  • Updated package documentation to support roxygen2 7.0 update.
  • Reworked formalsList global slightly. Using the synesthesia color palette for heatmap.color argument doesn’t always perform well enough, so I’m switching to a blue/black/yellow palette defined by blueYellow in acidplots instead for heatmap.color. The synesthesia palette performs really well for correlation heatmaps, and is now recommended by default via the acid.heatmap.correlation.color global now instead.
  • filterCells: Improved internal sampleName / sampleID handling.

basejump 0.11.24 (2020-01-08)

New functions:

  • integerCounts: Simple method support for returning a rounded integer counts matrix. Intended primarily for downstream handoff to bulk RNA-seq differential expression callers, such as DESeq2.

Minor changes:

  • Updated dependency package version requirements. Needed primarily for bug fix in transformer, improving mutateAll functionality.