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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`RangedSummarizedExperiment` cannot be stored in a `SummarizedExperiment`-only slot

#84 LTLA opened 1 week ago
1
Add saveRDS() method for SummarizedExperiment derivatives

#83 hpages closed 1 month ago
3
n x p

#82 ellispatrick opened 2 months ago
1
Coercion from SCE drops off rowData

#81 TuomasBorman opened 3 months ago
1
`?SummarizedExperiment` redirects to the docs for `RangedSummarizedExperiment`

#80 lazappi closed 1 month ago
5
Clarify withDimnames=FALSE in the documentation

#79 SamGG closed 10 months ago
3
add a section about interactive visualization

#78 kevinrue closed 1 year ago
1
Rows being removed from ASV table when building SummarizedExperiment

#77 yasminhilliam closed 1 year ago
0
Depreciated function calls in DelayedArray

#76 mingl1997 closed 1 year ago
4
Warning and error message when using '$' operator on summarizedExperiment object

#75 DijkJel closed 1 year ago
5
Warning about dim, nrow and ncol deprecated methods.

#74 charles-plessy opened 1 year ago
2
colData Default in Constructor Inconsistency

#73 DarioS opened 1 year ago
1
metadata function is not exported as others

#72 hsiaoyi0504 closed 1 year ago
1
Feature request: keep rownames(se) and rownames() of DataFrame nested in rowData(se) in sync

#71 kevinrue closed 1 year ago
4
Curious about how Rd manuals are generated

#70 mvfki closed 1 year ago
3
Add an `assaybind()` method

#69 multimeric opened 1 year ago
0
package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'SummarizedExperiment'

#68 bakaufman opened 1 year ago
1
Erroneous behaviour when colData is data.frame

#67 TuomasBorman opened 1 year ago
0
`combineCols` should keep names in metadata with `use.names=TRUE`

#66 LTLA opened 2 years ago
0
Remove all dimnames in `combine_assays_by` to avoid constructor check failures

#65 LTLA closed 2 years ago
3
`all.equal(x, y)` vs `all(x == y)`

#64 LiNk-NY closed 2 years ago
3
Constructor could check that assay is in matric format

#63 TuomasBorman closed 2 years ago
2
Consider assayData DataFrame for assays

#62 jmw86069 closed 2 years ago
6
`combineCols()` and `combineRows()` not listed in 'Usage' section

#61 PeteHaitch closed 2 years ago
4
Enforce unique assay names

#60 hpages opened 2 years ago
2
Should the show() method for SummarizedExperiment objects suggest saveHDF5SummarizedExperiment()?

#59 hpages opened 3 years ago
1
subset fails when subsetting a SummarizedExperiment object with no samples

#58 kpagacz closed 3 years ago
11
Adding checkDimnames=FALSE to the SE constructor

#57 LTLA closed 3 years ago
1
Constructor assigns wrong assay values to wrong samples and features

#56 TuomasBorman closed 3 years ago
7
Subsetting

#55 antagomir closed 3 years ago
2
add dims note

#54 LiNk-NY closed 3 years ago
1
Add rownames check for cbind()

#53 tavareshugo opened 3 years ago
0
Vignette Doesn't Specify Dimensionality Rules

#52 DarioS closed 3 years ago
1
assay<- is too pedantic when the dimensions are named

#51 LTLA closed 3 years ago
2
Add a showAsCell method for SummarizedExperiment objects

#50 LTLA closed 3 years ago
1
Conversion to SingleCellExpriment object

#49 zhli12 closed 3 years ago
1
Migrate SCE's flexible row combiner for general SE use.

#48 LTLA closed 3 years ago
10
fail to create `rbind` for SE-derived class due to the validity check

#47 fionarhuang closed 3 years ago
2
More informative error message for mismatching numbers of rows

#46 LTLA opened 4 years ago
0
Add utility to easily split rows/columns by a factor.

#45 LTLA closed 4 years ago
1
loading package taking too much memory

#44 spocks opened 4 years ago
2
Coercion from SummarizedExperiment to ExpressionSet creates an unlocked environment

#43 tomsing1 closed 4 years ago
3
“SimpleAssays” is not a defined class

#42 Georgy415 closed 4 years ago
2
Incorrect document page

#41 Jiefei-Wang closed 4 years ago
2
Improving the performance when calling assays accessor on a SummarizedExperiment object?

#40 Jiefei-Wang closed 4 years ago
2
Type conversion btw SimpleAssays and list

#39 Jiefei-Wang closed 4 years ago
2
a = SimpleList(setNames(nm = list())); assays(SummarizedExperiment(a)) is no longer endomorphic

#38 mtmorgan closed 4 years ago
6
error object 'normalize_names_replacement_value' not found

#37 weibei43 closed 4 years ago
9
colData assignment should fail but does not

#36 vjcitn opened 4 years ago
1
colnames-related concerns

#35 vjcitn closed 4 years ago
5