Major changes:
FGSEAList
class to FgseaList
.export
method to conform to new changes in pipette package.
Namely, we have reworked the generic to be simpler than BiocIO variant.Minor changes:
Major changes:
DFrame
instead of DataFrame
virtual class, where
applicable.GRanges
directly instead of GenomicRanges
virtual class,
where applicable.Minor changes:
requireNamespaces
import from AcidBase to goalie.Major changes:
export
: Restricting methods, following conventions now defined in pipette
0.10.0 update.hasDuplicates
internally from goalie.Major changes:
RankedList
Relaxed the internal thresholds for acceptable gene identifier
mapping thresholds. Previous cutoffs were a bit too strict and could result
in errors with acceptable datasets.export
: Simplified S4 method to class with con
and format
arguments
defined as required character
and missingOrNULL
, respectively. Improved
the documentation to denote that user should specify a directory as con
, and
either "csv"
or "tsv"
as the desired output format
.Minor changes:
markdownlint
.Major changes:
FGSEAList
: Simplified input to use recommended defaults for fgsea
passthrough. Note that fgsea now uses fgseaMultilevel
by default in
Bioconductor 3.15. Object class checks have been updated to reflect this
breaking change.Minor changes:
RankedList
: Fix for ensemblId
handling as input.fgsea
object.Minor changes:
tempdir2
and unlink2
.Major changes:
RankedList
: Improved keyType
support, adding back "geneId"
, and
"ensemblId"
. Simplified internal code for unlisting nested Entrez identifier
keys and ensuring they map 1:1 by oldest identifier.RankedList
: Function now looks inside geneId
and checks against provider
metadata defined in rowRanges
, in the event that ensemblId
or ensemblId
mcols
are not defined, but the key is in Ensembl or Entrez format.RankedList
: In the event the user requests keyType
of "geneId"
or
"ensemblId"
, we now also call stripGeneVersions
to sanitize the
gene identifiers to remove gene versions.Major changes:
topTables
as markdownTables
, following updated conventions used
in other Acid Genomics packages, such as AcidMarkdown and DESeqAnalysis.Minor changes:
Major changes:
Major changes:
plotNES
, plotGeneSet
, results
.export
method now confirms to BiocIO approach, using con
argument.RankedList
: Tightned up Ensembl reference genome filtering, checking for
gene identifiers from primary chromosomes, to avoid unwanted averaging of
values from haplotype scaffold gene identifiers. Also added support for
proteinCodingOnly
, to enable analysis of protein coding genes only, which
is disabled by default.Minor changes:
FGSEAList
and RankedList
: Reworked default formals for keyType
and value
.RankedList
S4 class.fgsea
handoff.plotLFC
: Improved labeling of axes.prepareGeneSetFiles
: Reworked file name detection for MSigDb.Minor changes:
RankedList
: Improved handling of duplicate Entrez gene identifiers, such
as is the case in the bcbioRNASeq F1000 example dataset.Minor changes:
RankedList
: Improved column name sanitization and handling for input
DESeqResults
object, avoiding conflicts with Gene2Symbol
object.~/msigdb
.Minor changes:
fgsea
object (FGSEAList
).New functions:
prepareGeneSetFiles
: MSigDb utility function for easy matching of default
GMT gene files to use for GSEA. Matches the symbol files by default.Major changes:
RankedList
and FGSEAList
method support has been improved for minimal
DESeqResults
and DataFrame
objects. These approaches are intended
primarily for analysis of files from collaborators where we don't necessarily
have the complete set of DESeq2 analysis files, and therefore cannot
construct a DESeqAnalysis
object.Minor changes:
RankedList
now supports keyType
, which defaults to gene name (a.k.a.
symbol), but now also supports original gene identifier. This alternative
option is useful when working with the clusterProfiler package and is used
in the bcbioRNASeq template.Major changes:
Major changes:
Minor changes:
geneSetNames
, plotLFC
, plotNES
.Major changes:
FGSEAList
: Reworked primary method to use DESeqAnalysis
instead of
RankedList
as input. The RankedList
object is now calculated automatically
internally.FGSEAList
object.gmtFiles
argument has been renamed to geneSetFiles
.New functions:
geneSetResults
: Extract gene set expression values (from DESeqResults
).leadingEdge
: New accessor that returns leading edge genes from GSEA run.results
: Extract GSEA results from object (from fgsea
return).Major changes:
alphaThreshold
and nesThreshold
S4 generic support.New functions:
plotGeneSet
: Split out internal gene set plotting code used previously in
plotEnrichedGeneSets
. This is a modified variant of fgsea::plotEnrichment
that allows for additional color customization.Major changes:
plotEnrichedGeneSets
: Now calls new plotGeneSet
function internally.Minor changes:
plotCounts
method, in favor of plotHeatmap
usage.Major changes:
FGSEAList
: Converted function to an S4 generic. Previously the main arguemnt
was named rankedList
, but this has been renamed to object
. A RankedList
object can still be passed in as the first object in the function call. This
change was necessary for adding GSEA support in pointillism single-cell
RNA-seq analysis toolkit.Minor changes:
RankedList
: Added support for DataFrame
class, which is used inside
pointillism package update.RankedList
: Added gene2symbol
argument support for matrix
model.
Using this for cluster matrix in pointillism for scRNA-seq using output
from edgeR (or DESeq2) for per-cluster marker analysis.Minor changes:
setValidity
from setClass
for S4 class definitions.updateObject
: Added support for ...
and verbose
arguments defined in the
S4 generic.Major changes:
enrichedGeneSets
, plotEnrichedGeneSets
,
and plotEnrichedUpset
.Minor changes:
convertToHuman
: Updated working example to use Ensembl 99 release, as
archived releases are currently unavailable via biomaRt until March 24, due
to Ensembl server migration. See Ensembl website for details.gsea
object.Minor changes:
Minor changes:
New functions:
plotCounts
, plotHeatmap
: Added initial FGSEAList
method support.Major changes:
plotGSEATable
: Made defunct, since this visualization doesn't render very
reliably in R Markdown output. Consider using a heatmap approach instead.Minor changes:
export
: Updated internal code to handle leadingEdge
as list
class.Major changes:
DataFrame
rather than data.table
.Minor changes:
Minor changes:
New functions:
convertToHuman
: Utility that maps orthologs onto human genes, so we can
perform GSEA. Added map
argument support, to speed up multiple calls.New functions:
convertToHuman
, which allows for easy ortholog
conversion to HUGO (HGNC) identifiers.Minor changes:
render.R
script for looping multiple DESeqAnalysis
objects.export
method.Major changes:
collectionNames
instead of pathwayNames
.enriched
and plotEnrichedUpset
have been updated to return per collection
(e.g. hallmark gene set), which makes more sense. We don't want to visualize
overlap across collections, since these are often completely different
classes (e.g. c1-c7 will never have overlap).New functions:
pathwayNames
, contrastNames
: Accessor functions for pathway (e.g. MSigDb)
and differential expression contrast names.enriched
method support for FGSEAList class. Useful for returning a list
directionally significant pathways, per contrast. Primarily intended for use
at the moment with plotEnrichedUpset
.plotEnrichedUpset
: Utility function that makes it easy to compare enrichment
groups across contrasts, via an UpSet plot.Major changes:
combine
method support for FGSEAList
, allowing us to easily combine
GSEA results from multiple datasets. Primarily intended for downstream
visualization using an UpSet plot (see plotEnrichedUpset
).Minor changes:
show
method support for FGSEAList
, showing pathwayNames
and
contrastNames
more clearly.Minor changes:
Minor changes:
theme_paperwhite
to acid_theme_light
.Minor changes:
rnaseq
Docker image.Major changes:
list
to FGSEAList
coercion method.Minor changes:
pfgsea
: Renamed bpparam
argument to BPPARAM
, to match Bioconductor.
Also now reexporting BiocParallel::bpparam
.gsea
minimal working example dataset, for unit testing.gsea
data.theme_paperwhite
. Now reexporting this function.Minor changes:
theme_paperwhite
from minimalism package.Minor changes:
Minor changes:
Major changes:
FGSEAList
and RankedList
S4 classes.plotEnrichment()
, plotGSEATable()
, and topTables()
to use
FGSEAList
object.statsList()
to RankedList()
, and switched to S4 method approach.Minor changes:
New functions:
Major changes:
Major changes:
Minor changes:
Initial release.
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