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agglomeration functions and na.rm #658

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merged 18 commits into from
Nov 15, 2024
Merged

agglomeration functions and na.rm #658

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TuomasBorman Nov 8, 2024
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TuomasBorman Nov 8, 2024
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TuomasBorman Nov 11, 2024
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TuomasBorman Nov 11, 2024
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TuomasBorman Nov 11, 2024
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TuomasBorman Nov 11, 2024
6b65902
Fix Bioc warnings
TuomasBorman Nov 11, 2024
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TuomasBorman Nov 11, 2024
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TuomasBorman Nov 14, 2024
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TuomasBorman Nov 14, 2024
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TuomasBorman Nov 14, 2024
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TuomasBorman Nov 14, 2024
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TuomasBorman Nov 14, 2024
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TuomasBorman Nov 14, 2024
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TuomasBorman Nov 15, 2024
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TuomasBorman Nov 15, 2024
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TuomasBorman Nov 15, 2024
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TuomasBorman Nov 15, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,6 +1,6 @@
Package: mia
Type: Package
Version: 1.15.4
Version: 1.15.5
Authors@R:
c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
email = "[email protected]",
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3 changes: 2 additions & 1 deletion NAMESPACE
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Expand Up @@ -289,7 +289,9 @@ importFrom(DelayedArray,DelayedArray)
importFrom(DelayedArray,colSums)
importFrom(DelayedArray,getAutoBPPARAM)
importFrom(DelayedArray,rowSums)
importFrom(DelayedArray,rowsum)
importFrom(DelayedArray,setAutoBPPARAM)
importFrom(DelayedArray,type)
importFrom(DelayedMatrixStats,colMeans2)
importFrom(DelayedMatrixStats,colQuantiles)
importFrom(DelayedMatrixStats,colSums2)
Expand Down Expand Up @@ -375,7 +377,6 @@ importFrom(rbiom,unifrac)
importFrom(rlang,":=")
importFrom(rlang,sym)
importFrom(scuttle,sumCountsAcrossFeatures)
importFrom(scuttle,summarizeAssayByGroup)
importFrom(stats,TukeyHSD)
importFrom(stats,anova)
importFrom(stats,as.dist)
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1 change: 1 addition & 0 deletions NEWS
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Expand Up @@ -159,3 +159,4 @@ computation

Changes in version 1.15.x
+ subsetBy*: added update.tree argument
+ agglomerateBy*: Add na.rm option for excluding NA counts
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