DepMapAnalysis
and Achilles
objects have been dropped
in favor of simply using GeneEffect
object class.Codependencies
class, which imports the top 100
co-dependencies for a gene from DepMap.plotGeneEffectVsExpression
.plotTopGeneEffectPerGroup
: Added a new plotting function that makes it
easier to visualize gene effects (dependency scores) across a subset of
cell lines, such as specific lineages (solid tumors, blood cancer, etc.).Achilles
S4 class definition remains exported, to maintain
better backward compatibility with objects saved prior to v0.1.0 release,
where we switched to DepMapAnalysis
object as the primary class for
analysis of Broad Achilles data.plotGeneEffect
: Added support for violin geom, and improved consistency
of ggplot2, using a switch
call internally.DepMapAnalysis
for both CRISPR and RNAi
gene effect datasets. Previously, these were classed as Achilles
and
DEMETER2
, which is confusing. Now both CRISPR and RNAi experiments keep
track of project source and scoring method more clearly.SummarizedExperiment
instead of DataFrame
, when possible.Achilles
object to inherit from SummarizedExperiment
instead of
RangedSummarizedExperiment
.DEMETER2
class objects now support colData
and rowData
.Achilles
: Gene synonyms are now fetched automatically, based on the new
makeGRangesFromEnsembl
update in basejump.cacheURL
function
defined in pipette package.plotGeneEffect
: Plot effect of gene knockdown as a boxplot or density plot.Achilles
object now requires slotting of common essential genes from DepMap.
These are now imported automatically in the main Achilles()
call.Initial release.
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