Bioconductor SummarizedExperiment issues

Bioconductor / SummarizedExperiment

A container (S4 class) for matrix-like assays

https://bioconductor.org/packages/SummarizedExperiment

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issues

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Resolve _R_CHECK_LENGTH_1_LOGIC2_ issue

#34 LiNk-NY closed 4 years ago
2
Slightly relaxing the rowData checks for cbind

#33 LTLA opened 4 years ago
0
Build an assay element to work from my own normalized count matrix

#32 ramarquezo closed 5 years ago
5
Extraction isn't working with ShallowSimpleListAssays on Bioc Devel 3.10

#31 mjsteinbaugh closed 5 years ago
4
Should `rowData` be merged with `mcols(gr)`?

#30 LiNk-NY opened 5 years ago
2
derived RSE to SE coercion discards names

#29 LTLA opened 5 years ago
15
seqinfo<-() fails when @rowData is a GRangesList

#28 lawremi closed 5 years ago
2
c() does not work on SummarizedExperiment

#27 lawremi opened 5 years ago
1
SummarizedExperiment R package not allowing installation.

#26 joao1980 closed 4 years ago
8
assayNames<- is reluctant to work

#25 LTLA closed 5 years ago
5
Why is SummarizedExperiment graphic not directly included in package?

#24 PeteHaitch closed 5 years ago
4
SummarizedExperiment::cbind

#23 tiagochst opened 5 years ago
3
Implement an all.equal() method for SummarizedExperiment objects that performs a "deep comparison"

#22 hpages opened 5 years ago
0
Stop wrapping the user-supplied assays in a ref object when storing them in the "assays" slot of a SummarizedExperiment object

#21 hpages closed 5 years ago
1
Convert ShallowSimpleListAssays into an S3 list

#20 marcpaga closed 5 years ago
3
Allow clearing of colData

#19 LTLA closed 5 years ago
1
Added SE coercion advice to derivation vignette

#18 LTLA closed 5 years ago
1
SummarizedExperiment doesn't work with data.frame input

#17 LTLA closed 5 years ago
4
all.equal does not work for SE objects

#16 LTLA closed 5 years ago
5
Advised on implementation of SE coercion methods

#15 LTLA closed 6 years ago
1
Error in coercion SummarizedExperiment <-> ExpressionSet

#14 lgeistlinger closed 6 years ago
1
rowData rownames issue explored at BioC2018

#13 mikelove opened 6 years ago
6
Use DelayedArray:::set_dimnames() in realize,SummarizedExperiment-method

#12 PeteHaitch closed 6 years ago
2
Fix 'getter' example in 'Extensions' vignette

#11 PeteHaitch closed 6 years ago
1
Detailed instructions for class extension

#10 LTLA closed 6 years ago
23
Add BACKEND argument to realize,SummarizedExperiment-method

#9 PeteHaitch closed 6 years ago
0
SummarizedExperiment() constructor with SummarizedExperiment given as argument should return the same SummarizedExperiment

#8 dvantwisk closed 3 years ago
5
Difficult bug when colnames are arrays

#7 LTLA closed 6 years ago
6
addition of explicit subset method for SummarizedExperiment class

#6 schifferl closed 6 years ago
0
import / export as loom

#5 mtmorgan closed 6 years ago
1
Fix broken link to SummarizedExperiment doc

#4 LiNk-NY closed 6 years ago
0
HDF5ArraySeed slot name 'filepath' instead of 'file'.

#3 Liubuntu closed 6 years ago
1
rowData does not contain the rownames

#2 LTLA closed 6 years ago
34
More informative errors for assay() with names.

#1 LTLA closed 6 years ago
0