Changelog
Source:NEWS.md
AcidGenerics 0.7.9 (2025-03-21)
Minor changes:
- Relaxed R dependency down to 4.0 for better backwards compatibility on legacy systems, such as Ubuntu 22 LTS.
AcidGenerics 0.7.7 (2024-03-18)
New functions:
-
stripExonVersions
: New generic similar tostripGeneVersions
andstripTranscriptVersions
.
AcidGenerics 0.7.6 (2023-12-15)
New functions:
-
matchAll
: New variant ofmatch
that returns all positional matches for arguments defined inx
, 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 asDFrameList
toDFrame
.
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
toplotFeatureSaturation
. - Removed
plotCountsPerGene
in favor ofplotCountsPerFeature
. - Removed
topTables
in favor ofmarkdownTables
.
AcidGenerics 0.7.1 (2023-10-03)
Major changes:
- Fixed some additional generics that should be in strict camel case.
- Renamed
convertSampleIDsToNames
toconvertSampleIdsToNames
. - Renamed
geneIDs
togeneIds
. - Renamed
mapGenesToIDs
tomapGenesToIds
. - Renamed
transcriptIDs
totranscriptIds
.
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
toEnsemblToNcbi
. - Renamed
Gene2Symbol
toGeneToSymbol
. - Renamed
Ncbi2Ensembl
toNcbiToEnsembl
. - Renamed
Tx2Gene
toTxToGene
. - Renamed
cell2sample
tocellToSample
. - Renamed
plotDEGHeatmap
toplotDegHeatmap
. - Renamed
plotDEGPCA
toplotDegPca
. The word boundary is better here. - Renamed
plotDEGStackedBar
toplotDegStackedBar
. - Renamed
plotDEGUpset
toplotDegUpset
. - Renamed
plotLFC
toplotLfc
. - Renamed
plotNES
toplotNes
. - Renamed
plotPCACovariates
toplotPcaCovariates
. - Renamed
plotPCElbow
toplotPcElbow
. - Renamed
plotQC
toplotQc
. - Renamed
plotRRNAMappingRate
toplotRrnaMappingRate
. The word boundary looks clearer to me here. - Renamed
plotTSNE
toplotTsne
. - Renamed
plotUMAP
toplotUmap
. - Renamed
removeNA
toremoveNa
. - Renamed
sanitizeNA
tosanitizeNa
. - Now exporting
plotMa
andplotPca
strict camel variants. BiocGenerics usesplotMA
andplotPCA
, 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 ourfactorize
generic. - Added simpler variants of BiocIO
import
andexport
.
AcidGenerics 0.6.11 (2023-09-12)
Major changes:
- Migrated functions from DepMapAnalysis package:
excludeContaminatedCells
,excludeProblematicCells
,plotGeneEffect
,plotGeneEffectVsExpression
,plotTopGeneEffectPerCell
,plotTopGeneEffectPerGroup
,predictSensitivity
,selectCells
,tnbc
.
AcidGenerics 0.6.9 (2023-09-08)
New functions:
-
keepOnlyAtomicCols
: New generic with methods that will be defined in AcidBase forDFrame
anddata.frame
classes.
AcidGenerics 0.6.8 (2023-08-23)
New functions:
-
unnest2
: Our simpler S4 generic variant oftidyr::unnest
.
AcidGenerics 0.6.7 (2023-04-12)
New functions:
-
Ensembl2Ncbi
,Ncbi2Ensembl
, andmatchNested
.
Minor changes:
- Deprecated
Ensembl2Entrez
andEntrez2Ensembl
in favor ofEnsembl2Ncbi
andNcbi2Ensembl
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 onlyrbindToDataFrame
.
AcidGenerics 0.6.5 (2022-11-17)
New functions:
-
euclidean
andzscore
. For use in pending AcidBase package update.
AcidGenerics 0.6.4 (2022-09-16)
New functions:
-
cast
: the opposite ofmelt
. Using the naming conventions defined in now deprecated reshape2 package.
AcidGenerics 0.6.3 (2022-05-25)
New functions:
- Reworking
markdownPlots
andmarkdownTables
as S4 generics. Previously these used a basiclist
argument in AcidMarkdown package, but these generics are useful in other bioinformatics packages. - Soft deprecating
topTables
in favor ofmarkdownTables
usage.
AcidGenerics 0.6.2 (2022-05-11)
New functions:
- Added
as.Seurat
andas.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
andimport
generics to inherit from new BiocIO package. - Migrated generics from AcidGenomes:
Ensembl2Entrez
,Entrez2Ensembl
,Gene2Symbol
, andTx2Gene
. - Migrated new generics defined in DESeqAnalysis package:
plotContrastScatter
andplotLFC
. - Migrated
KnownMarkers
generic from AcidSingleCell here.
Minor changes:
- Reworked documentation for
as.DataFrame
generic. - Include
GRanges
andGRangesList
generators from GenomicRanges package. - Also reexporting new
BiocFile
class from BiocIO package. - Now including additional reexports from GenomeInfoDb package:
Seqinfo
,genome
,seqinfo
,seqlevels
, andseqnames
. 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
, andunlistToDataFrame
.
AcidGenerics 0.5.18 (2021-06-20)
New functions:
- Reexporting
median
andquantile
, which are defined in IRanges. These generics are very useful when operating onNumericList
objects.
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
andrbindToDataFrame
, which have methods (i.e. forlist
) defined in AcidPlyr update.
Minor changes:
- Deprecating
unlistToDataFrame
in favor ofmapToDataFrame
.
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
, andwidth
from BiocGenerics. - Also reexporting
grep
andgrepl
from BiocGenerics, which is needed for downstream operations onCharacterList
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 0.5.9 (2021-02-09)
New functions:
- Reexporting some additional Bioconductor generics:
head
,summary
,tail
. -
plotCorrelation
: New X-Y scatterplot correlation plotting generic.
AcidGenerics 0.5.6 (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
andshowHeader
, 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 bymean
andsem
.
AcidGenerics 0.5.2 (2021-01-21)
New functions:
-
geneIDs
(complementing previousgeneNames
generic),transcriptIDs
,transcriptNames
,stripGeneVersions
, (complementing previousstripTranscriptVersions
generic), and a newstripVersions
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
, andmatchTranscriptColumn
.
Deprecations:
- Deprecated
matchRowNameColumn
in favor ifmatchRownameColumn
(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
andsampleNames<-
generics. - Migrated some generics previously defined in basejump:
integerCounts
,makeSampleData
. - Need to reexport
colSums
,rowSums
, andunlist
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
, andslotAlignedCounts
. - 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 0.3.14 (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
, andplotNES
. - Added new mapping generics:
mapColnames
,mapRownames
. - Added additional mapping generics in use by new cellosaurus and DepMapAnalysis packages:
mapCells
andmapGenes
.
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
, andtransformType
.
acidgenerics 0.3.5 (2020-05-21)
Minor changes:
- Removed unused
rankedList
generic. Note that acidgenerics package usesRankedList
generic instead. - Removed unused
pseudobulk
generic. UsingaggregateCellsToSamples
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 inaggregate
generic. -
aggregateCellsToSamples
,aggregateReplicates
: Also switched from “object” to “x” here, matchingaggregate
convention. - Removed unused
aggregateReplicates
generic.
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
, andupperCamelCase
.
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
, andmetadata2
.