NEWS.md

In acidgenomics/bioverbs: Acid Genomics Generics

Release notes

AcidGenerics 0.7.8 (2024-04-05)

New functions:

• plotCleveland: Cleveland dot plot generic.

AcidGenerics 0.7.7 (2024-03-18)

New functions:

• stripExonVersions: New generic similar to stripGeneVersions and stripTranscriptVersions.

AcidGenerics 0.7.6 (2023-12-15)

New functions:

• matchAll: New variant of match that returns all positional matches for arguments defined in x, rather than only the first match.

AcidGenerics 0.7.5 (2023-12-12)

New functions:

• filterNested: Keep rows that match a nested condition. Performs recursive regular expression matching across all columns, including nested list columns.

AcidGenerics 0.7.4 (2023-11-30)

New functions:

• unlist2: Unlist a complex S4 object, such as DFrameList to DFrame.

AcidGenerics 0.7.3 (2023-10-06)

New functions:

• cellsPerGeneFusion: Return the number of cells per gene fusion.
• cellsPerMutation: Return the number of cells per mutation.
• excludeNonCancerCells: Exclude non-cancer cells.
• excludeNonHumanCells: Exclude non-human cells.
• geneFusions: Gene fusions per cell.
• mutations: (Driver gene) mutations per cell.

AcidGenerics 0.7.2 (2023-10-05)

Major changes:

• Renamed plotGeneSaturation to plotFeatureSaturation.
• Removed plotCountsPerGene in favor of plotCountsPerFeature.
• Removed topTables in favor of markdownTables.

AcidGenerics 0.7.1 (2023-10-03)

Major changes:

• Fixed some additional generics that should be in strict camel case.
• Renamed convertSampleIDsToNames to convertSampleIdsToNames.
• Renamed geneIDs to geneIds.
• Renamed mapGenesToIDs to mapGenesToIds.
• Renamed transcriptIDs to transcriptIds.

AcidGenerics 0.7.0 (2023-09-29)

Major changes:

• New release series where we are enforcing strict camel case for all generics.
• Also removed usage of "2" in generic names in favor of "to".
• Renamed Ensembl2Ncbi to EnsemblToNcbi.
• Renamed Gene2Symbol to GeneToSymbol.
• Renamed Ncbi2Ensembl to NcbiToEnsembl.
• Renamed Tx2Gene to TxToGene.
• Renamed cell2sample to cellToSample.
• Renamed plotDEGHeatmap to plotDegHeatmap.
• Renamed plotDEGPCA to plotDegPca. The word boundary is better here.
• Renamed plotDEGStackedBar to plotDegStackedBar.
• Renamed plotDEGUpset to plotDegUpset.
• Renamed plotLFC to plotLfc.
• Renamed plotNES to plotNes.
• Renamed plotPCACovariates to plotPcaCovariates.
• Renamed plotPCElbow to plotPcElbow.
• Renamed plotQC to plotQc.
• Renamed plotRRNAMappingRate to plotRrnaMappingRate. The word boundary looks clearer to me here.
• Renamed plotTSNE to plotTsne.
• Renamed plotUMAP to plotUmap.
• Renamed removeNA to removeNa.
• Renamed sanitizeNA to sanitizeNa.
• Now exporting plotMa and plotPca strict camel variants. BiocGenerics uses plotMA and plotPCA, for reference.

Minor changes:

• Reworked documentation to indicate that headtail should return character.

AcidGenerics 0.6.12 (2023-09-20)

New functions:

• Added unfactorize, the opposite of our factorize generic.
• Added simpler variants of BiocIO import and export.

AcidGenerics 0.6.11 (2023-09-12)

Major changes:

• Migrated functions from DepMapAnalysis package: excludeContaminatedCells, excludeProblematicCells, plotGeneEffect, plotGeneEffectVsExpression, plotTopGeneEffectPerCell, plotTopGeneEffectPerGroup, predictSensitivity, selectCells, tnbc.

AcidGenerics 0.6.10 (2023-09-11)

Minor changes:

• euclidean: Removed requirement of y in the generic.

AcidGenerics 0.6.9 (2023-09-08)

New functions:

• keepOnlyAtomicCols: New generic with methods that will be defined in AcidBase for DFrame and data.frame classes.

AcidGenerics 0.6.8 (2023-08-23)

New functions:

• unnest2: Our simpler S4 generic variant of tidyr::unnest.

AcidGenerics 0.6.7 (2023-04-12)

New functions:

• Ensembl2Ncbi, Ncbi2Ensembl, and matchNested.

Minor changes:

• Deprecated Ensembl2Entrez and Entrez2Ensembl in favor of Ensembl2Ncbi and Ncbi2Ensembl respectively. This generics will be updated in a forthcoming package update to AcidGenerics.

AcidGenerics 0.6.6 (2023-02-09)

Minor changes:

• Removed now unused mapToDataFrame, in favor of only rbindToDataFrame.

AcidGenerics 0.6.5 (2022-11-17)

New functions:

• euclidean and zscore. For use in pending AcidBase package update.

AcidGenerics 0.6.4 (2022-09-16)

New functions:

• cast: the opposite of melt. Using the naming conventions defined in now deprecated reshape2 package.

AcidGenerics 0.6.3 (2022-05-25)

New functions:

• Reworking markdownPlots and markdownTables as S4 generics. Previously these used a basic list argument in AcidMarkdown package, but these generics are useful in other bioinformatics packages.
• Soft deprecating topTables in favor of markdownTables usage.

AcidGenerics 0.6.2 (2022-05-11)

New functions:

• Added as.Seurat and as.SingleCellExperiment S4 generics, which are now in use in our pointillism package. Don't reexport these in basejump, as these are also defined as S3 generics in Seurat package.

AcidGenerics 0.6.1 (2022-04-29)

Major changes:

• Now pinning against R 4.2 as minimum dependency, for Bioconductor 3.15 release.

AcidGenerics 0.6.0 (2022-03-10)

Major changes:

• Package now requires R 4.1 and Bioconductor 3.14 release.
• Reworked export and import generics to inherit from new BiocIO package.
• Migrated generics from AcidGenomes: Ensembl2Entrez, Entrez2Ensembl, Gene2Symbol, and Tx2Gene.
• Migrated new generics defined in DESeqAnalysis package: plotContrastScatter and plotLFC.
• Migrated KnownMarkers generic from AcidSingleCell here.

Minor changes:

• Reworked documentation for as.DataFrame generic.
• Include GRanges and GRangesList generators from GenomicRanges package.
• Also reexporting new BiocFile class from BiocIO package.
• Now including additional reexports from GenomeInfoDb package: Seqinfo, genome, seqinfo, seqlevels, and seqnames. This are used primarily in the AcidGenomes and AcidGSEA packages.

AcidGenerics 0.5.20 (2021-09-08)

Minor changes:

• Removing deprecated functions from the NAMESPACE, to clean up and lighten the package a bit: clusterCellCountsPerSample, flatFiles, markdown, matchRowNameColumn, mcolnames, meltCounts, plotDot, plotGSEATable, plotGenesDetected, plotGenesPerCell,plotUMIsPerCell, plotUMIsVsGenes, and unlistToDataFrame.

AcidGenerics 0.5.19 (2021-08-24)

Minor changes:

• Now requiring Bioconductor 3.13+ to be installed.

AcidGenerics 0.5.18 (2021-06-20)

New functions:

• Reexporting median and quantile, which are defined in IRanges. These generics are very useful when operating on NumericList objects.

AcidGenerics 0.5.17 (2021-02-22)

New functions:

• Reexporting sapply, which is used in pointillism.

AcidGenerics 0.5.16 (2021-02-22)

New functions:

• Including getListElement from S4Vectors, which is used in bcbioRNASeq.

AcidGenerics 0.5.15 (2021-02-20)

New functions:

• Now exporting mapToDataFrame and rbindToDataFrame, which have methods (i.e. for list) defined in AcidPlyr update.

Minor changes:

• Deprecating unlistToDataFrame in favor of mapToDataFrame.

AcidGenerics 0.5.14 (2021-02-13)

Minor changes:

• Added more Bioconductor generic reexports.
• Reorganized Bioconductor generics with roxygen documentation.

AcidGenerics 0.5.13 (2021-02-12)

Major changes:

• Now including IRanges in package.
• Including more reexports that are defined in S4Vectors and BiocGenerics.

AcidGenerics 0.5.12 (2021-02-12)

Minor changes:

• Now reexporting end, start, and width from BiocGenerics.
• Also reexporting grep and grepl from BiocGenerics, which is needed for downstream operations on CharacterList in AcidGenomes.

AcidGenerics 0.5.11 (2021-02-11)

Minor changes:

• Consolidate all S4Vectors class and function reexports here. Some were previously defined in pipette.

AcidGenerics 0.5.10 (2021-02-10)

New functions:

• Reexporting cbind and rbind from Bioconductor.

AcidGenerics 0.5.9 (2021-02-09)

New functions:

• Reexporting some additional Bioconductor generics: head, summary, tail.
• plotCorrelation: New X-Y scatterplot correlation plotting generic.

AcidGenerics 0.5.8 (2021-02-08)

New functions:

• Include var reexport, which is used in AcidPlots.

AcidGenerics 0.5.7 (2021-02-08)

New functions:

• Reexporting unsplit from BiocGenerics.

AcidGenerics 0.5.6 (2021-02-05)

New classes:

• Exporting missingOrNULL class, previously defined internally in basejump.
• Also now reexporting Annotated class from S4Vectors.

AcidGenerics 0.5.5 (2021-02-02)

New generics:

• Created new generics for rankedMatrix and showHeader, which are now defined in AcidBase. Previously, these functions were defined in basejump.

Minor changes:

• geometricMean: Renamed primary argument from "object" to "x", better matching the conventions used by mean and sem.

AcidGenerics 0.5.4 (2021-02-02)

Major changes:

• Made markdown and mcolnames generics defunct.

AcidGenerics 0.5.3 (2021-01-25)

Minor changes:

• Reexporting is.unsorted and sort from BiocGenerics.

AcidGenerics 0.5.2 (2021-01-21)

New functions:

• geneIDs (complementing previous geneNames generic), transcriptIDs, transcriptNames, stripGeneVersions, (complementing previous stripTranscriptVersions generic), and a new stripVersions generic that is intended to sanitize both genes and transcripts in a single call.

AcidGenerics 0.5.1 (2021-01-15)

New functions:

• Added some useful matching generics, which will be deployed in Acid Generics packages to avoid hard-coding identifier column names: matchCellColumn, matchGeneColumn, matchSampleColumn, and matchTranscriptColumn.

Deprecations:

• Deprecated matchRowNameColumn in favor if matchRownameColumn (note case).

AcidGenerics 0.5.0 (2020-12-22)

Major changes:

• Now reexporting S4 generics defined in BiocGenerics and S4Vectors that are used to define methods inside Acid Genomics R packages.
• Importing Biobase package, which defines sampleNames and sampleNames<- generics.
• Migrated some generics previously defined in basejump: integerCounts, makeSampleData.
• Need to reexport colSums, rowSums, and unlist from BiocGenerics.
• Now importing AsIs S4 class defined in BiocGenerics.
• Importing additional S4 generics defined in S4Vectors that are in use internally inside basejump.
• Migrated generics previously defined in bcbioRNASeq: as.DESeqDataSet, as.DESeqTransform, as.DGEList, plotPseudoVsAlignedCounts, and slotAlignedCounts.
• Added unlistToDataFrame, which is being added to AcidPlyr.

AcidGenerics 0.4.1 (2020-11-24)

New functions:

• sem: New generic for calculating standard error of the mean.

AcidGenerics 0.4.0 (2020-10-06)

Major changes:

• Renamed package from acidgenerics to AcidGenerics.

acidgenerics 0.3.14 (2020-10-01)

New functions:

• Created a new generic for standardizeCells, which is in use in cellosaurus and DepMapAnalysis packages.

acidgenerics 0.3.13 (2020-10-01)

New functions:

• Migrated additional generics from acidgsea: geneSetNames, plotLFC, and plotNES.
• Added new mapping generics: mapColnames, mapRownames.
• Added additional mapping generics in use by new cellosaurus and DepMapAnalysis packages: mapCells and mapGenes.

acidgenerics 0.3.12 (2020-09-21)

New functions:

• Migrated generics from acidgsea: convertToHuman, geneSet, geneSetResults, leadingEdge, nesThreshold, plotGeneSet.

acidgenerics 0.3.11 (2020-09-14)

New functions:

• splitByLevel: New generic for easy splitting by factor in a data frame.

acidgenerics 0.3.10 (2020-08-18)

New functions:

• degIntersection: Return DEGs ranked by number of intersections.
• intersectAll: Look for all intersections in a list.
• intersectionMatrix: Generate an intersection matrix from a list.
• degPerContrast: Migrated from DESeqAnalysis.

acidgenerics 0.3.8 (2020-08-04)

New functions:

• New generics migrated from DESeqAnalysis: baseMeanThreshold, lfcShrink, lfcShrinkType, plotBaseMean, plotDEGStackedBar, resultsDiff, and transformType.

acidgenerics 0.3.7 (2020-07-24)

Minor changes:

• Maintenance release, increasing R dependency to 4.0.

acidgenerics 0.3.7 (2020-06-25)

New functions:

• Added plotWaterfall generic.

acidgenerics 0.3.6 (2020-06-10)

New functions:

• Added plotStackedBarPlot generic.

acidgenerics 0.3.5 (2020-05-21)

Minor changes:

• Removed unused rankedList generic. Note that acidgenerics package uses RankedList generic instead.
• Removed unused pseudobulk generic. Using aggregateCellsToSamples in basejump package instead.

acidgenerics 0.3.4 (2020-01-30)

Minor changes:

• aggregateCols, aggregateRows: Renamed primary argument from "object" to "x", better matching the conventions used in aggregate generic.
• aggregateCellsToSamples, aggregateReplicates: Also switched from "object" to "x" here, matching aggregate convention.
• Removed unused aggregateReplicates generic.

acidgenerics 0.3.3 (2020-01-28)

Minor changes:

• Switched license from MIT to GPL-3.

acidgenerics 0.3.2 (2020-01-28)

Minor changes:

• Documentation fixes to pass CRAN release checks.

acidgenerics 0.3.1 (2020-01-27)

New functions:

• Migrated S4 generics previously defined in syntactic package: camelCase, capitalize, dottedCase, kebabCase, makeDimnames, makeLabel, makeNames, makeTitle, makeWords, sentenceCase, snakeCase, and upperCamelCase.

acidgenerics 0.3.0 (2020-01-18)

Major changes:

• Renamed package from bioverbs to acidgenerics, in preparation for CRAN submission of multiple Acid Genomics R packages.
• Migrated S4 generics previously defined in now archived transformer package: as.DataFrame, as.SummarizedExperiment, coerceToList, matchRowNameColumn, and metadata2.

bioverbs 0.2.13 (2020-01-03)

Deprecated:

• plotDot deprecated in favor of plotDots, to match the naming convention currently used in the scater package.

bioverbs 0.2.12 (2019-11-19)

New functions:

• Added plotUpset generic. Corresponding methods for data.frame and DataFrame will be defined in acidplots update.

Minor changes:

• Made plotGSEATable defunct, which doesn't work that well in pfgsea package and will be removed in next update.

bioverbs 0.2.11 (2019-11-08)

New functions:

• Added correlation generic, which is more flexible than default cor generic defined in stats and/or S4Vectors.

bioverbs 0.2.10 (2019-09-10)

New functions:

• Added contrastName<- assignment method generic.
• Added resultsNames<- assignment method generic.

bioverbs 0.2.9 (2019-09-09)

Major changes:

• Migrated syntactic generics to the syntactic package. This includes: camelCase, capitalize, dottedCase, kebabCase, snakeCase, upperCamelCase.
• Made flatFiles defunct in favor of coerceS4ToList usage.

bioverbs 0.2.8 (2019-09-03)

Minor changes:

• Improve DataFrame return consistency in documentation.

bioverbs 0.2.7 (2019-08-27)

Major changes:

• Updated R dependency to 3.6.

New functions:

• Deprecated meltCounts in favor of simply using melt. Note that reshape2::melt is deprecated in favor of tidyr::gather, so we're not conflicting with any activate tidyverse verbs here.
• Migrated join, mutate, and select generics defined in transformer. Tightened up the required signature arguments here.

bioverbs 0.2.6 (2019-08-23)

New functions:

• nonzeroRowsAndCols: Generic that allows for easy subsetting of non-zero rows and columns from an object.

bioverbs 0.2.5 (2019-08-12)

New functions:

• plotSums: Utility generic for plotting row and column sums of a matrix.

bioverbs 0.2.4 (2019-08-08)

Reworked some verbs to support changes in acidplots and pending bcbioSingleCell update.

New functions:

• plotCountsPerCell.
• plotCountsVsFeatures.
• plotFeaturesPerCell.

Deprecated functions:

• plotGenesPerCell to plotFeaturesPerCell.
• plotGenesDetected to plotFeaturesDetected.
• plotUMIsPerCell to plotCountsPerCell.
• plotUMIsVsGenes to plotCountsVsFeatures.

bioverbs 0.2.3 (2019-08-08)

New functions:

• Added calculateMetrics generic, which was previously defined as a standard function in bcbioSingleCell package. This verb is also applicable to the Chromium package, so we have migrated it here.

bioverbs 0.2.2 (2019-08-07)

Minor changes:

• plotCellTypesPerCluster: Added markers to signature.

bioverbs 0.2.1 (2019-08-05)

New functions:

• Added plotCells generic.
• Added cpm and tpm generics, which are defined in SingleCellExperiment.

Major changes:

• Deprecated clusterID generic in favor of clusters.

Minor changes:

• plotTopMarkers now includes markers argument in the generic.

bioverbs 0.2.0 (2019-07-23)

Bumped version to v0.2 release series to match update conventions defined in other basejump packages, in preparation of a new release candidate that may be suitable for Bioconductor submission.

New functions:

• plotCountsCorrelation and plotCountsCorrelationHeatmap: New utility generics for comparing count correlation across multiple datasets.

Major changes:

• Renamed syntactic name functions, including "*Case" where appropriate. camel to camelCase; kebab to kebabCase; snake to snakeCase; upperCamel to upperCamelCase. The shorthand variants will remain exported in the syntactic package.

bioverbs 0.1.20 (2019-07-17)

Minor changes:

• Documentation improvements, particularly for deprecated functions.

bioverbs 0.1.19 (2019-05-29)

New functions:

• aggregateReplicates: Generic intended for technical replicate (e.g. L001-L004) sample aggregation. Currently used in bcbioRNASeq.
• plotCountDensity: Generic currently used by bcbioRNASeq v0.2 release series.

Minor changes:

• Keeping plotCountsPerGene and plotGenesDetected generics exported, to provide backward compatibility support for bcbioRNASeq v0.2 release series.

bioverbs 0.1.18 (2019-05-06)

Major changes:

• export generic now uses object instead of x, following the style defined in rtracklayer, rather than rio. This change will primarily affect the brio package, but also currently has method support in DESeqAnalysis and pfgsea.

bioverbs 0.1.17 (2019-05-05)

Major changes:

• Now pinned against R >= 3.5.

Minor changes:

• Miscellaneous documentation improvements, to pass BiocCheck.
• Improved Travis and AppVeyor CI configuration.

bioverbs 0.1.16 (2019-04-30)

New functions:

• alphaThreshold, lfcThreshold: Convenience generics for use in pfgsea package. These generics may also be useful for DESeqAnalysis package in a future update.
• collectionNames, contrastNames: Generics previously defined in the pfgsea package. These may be generally useful in other contexts.
• enrichedGeneSets, plotEnrichedUpset, plotEnrichedGeneSets, plotGSEATable: Useful S4 generics previously defined in pfgsea package.

bioverbs 0.1.15 (2019-04-26)

New functions:

• plotDEGHeatmap: Currently in use in the DESeqAnalysis package.

bioverbs 0.1.14 (2019-04-23)

New functions:

• resultsMatrix. Currently in use in the DESeqAnalysis package.

bioverbs 0.1.13 (2019-04-19)

Deprecations:

• Made plotGene defunct in favor of plotCounts.
• Made plotCountsPerGene defunct in favor of plotCountsPerFeature, and plotGenesDetected defunct in favor of plotFeaturesDetected.

bioverbs 0.1.12 (2019-04-19)

New functions:

• plotCellCountsPerCluster. Used by pointillism.

Deprecations:

• Deprecated plotCountsPerGene in favor of plotCountsPerFeature. This allows for use in packages at transcript or enhancer (locus) level.

bioverbs 0.1.11 (2019-04-06)

New functions:

• mcolnames: Quickly access the column names of mcols slot.

bioverbs 0.1.10 (2019-03-23)

Minor changes:

• Removed extra formatting in documentation titles.

bioverbs 0.1.9 (2019-03-22)

Minor changes:

• Switched domain to Acid Genomics.

bioverbs 0.1.8 (2019-02-25)

New generics:

• fpkm.
• kebab.
• plotIntergenicMappingRate.

bioverbs 0.1.7 (2019-02-17)

New generics:

• pseudobulk.

Minor changes:

• plotGenderMarkers: Improved documentation to no longer point to plotGene.

bioverbs 0.1.6 (2019-02-11)

New generics:

• plotCounts.

Deprecations:

• plotGene is now deprecated in favor of plotCounts.

bioverbs 0.1.5 (2019-02-01)

New generics:

• rankedList.

bioverbs 0.1.4 (2019-01-12)

Minor changes:

• Added pkgdown website.

bioverbs 0.1.3 (2019-01-12)

New generics:

• atomize.
• factorize.

bioverbs 0.1.2 (2019-01-05)

Minor changes:

• Documentation improvements.

bioverbs 0.1.1 (2019-01-04)

Minor changes:

• Documentation fixes.
• Added Travis CI and AppVeyor CI code coverage support.

bioverbs 0.1.0 (2018-12-22)

Initial release. Migrated S4 generics from basejump and other bioinformatics-oriented packages here to define a simple, stable package similar to BiocGenerics.

acidgenomics/bioverbs documentation built on April 7, 2024, 7:14 a.m.