Bioconductor/SummarizedExperiment

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A container (S4 class) for matrix-like assays

Stars: 39
Forks: 11
Open beginner issues: 0
Indexed issues: 29

Dominant language: R
License: No license data
Last GitHub push: Apr 28, 2026
Latest indexed: Sep 21, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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29 open issues indexed

combineCols Exponential Slowdown Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

Bioconductor/SummarizedExperiment#99 · Opened Sep 10, 2026
Adding a new assay forces dimnames on all existing assays Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

Bioconductor/SummarizedExperiment#96 · Opened Aug 4, 2026
Adding data to row/colData Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

Bioconductor/SummarizedExperiment#92 · 3 comments · Opened Jan 26, 2026
Replacing colData with a named DataFrame silently misaligns assay columns when row order differs Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

Bioconductor/SummarizedExperiment#91 · Opened Jan 9, 2026
Subsetting SE with factor() does not work Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

Bioconductor/SummarizedExperiment#89 · 1 comment · Opened Sep 1, 2025
SE and RangeSE (and SCE) differences in accessing rowData Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Bioconductor/SummarizedExperiment#86 · 1 reaction · Opened Mar 8, 2025
longForm,SummarizedExperiment Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Bioconductor/SummarizedExperiment#85 · 3 comments · Opened Jan 26, 2025
`RangedSummarizedExperiment` cannot be stored in a `SummarizedExperiment`-only slot Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/SummarizedExperiment#84 · 1 comment · Opened Oct 31, 2024
n x p Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

Bioconductor/SummarizedExperiment#82 · 1 comment · Opened Sep 11, 2024
Coercion from SCE drops off rowData Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

Bioconductor/SummarizedExperiment#81 · 3 comments · Opened Jul 30, 2024
Warning about dim, nrow and ncol deprecated methods. Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Bioconductor/SummarizedExperiment#74 · 2 comments · Opened Jun 26, 2023
colData Default in Constructor Inconsistency Open

Bioconductor/SummarizedExperiment#73 · 1 comment · 1 assignee · Opened May 18, 2023
Add an `assaybind()` method Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

Bioconductor/SummarizedExperiment#69 · Opened Jan 16, 2023
package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'SummarizedExperiment' Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

Bioconductor/SummarizedExperiment#68 · 1 comment · Opened Jan 10, 2023
Erroneous behaviour when colData is data.frame Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

Bioconductor/SummarizedExperiment#67 · Opened Nov 29, 2022
`combineCols` should keep names in metadata with `use.names=TRUE` Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

Bioconductor/SummarizedExperiment#66 · Opened Nov 4, 2022
Enforce unique assay names Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Bioconductor/SummarizedExperiment#60 · 2 comments · Opened Jan 18, 2022
Should the show() method for SummarizedExperiment objects suggest saveHDF5SummarizedExperiment()? Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

Bioconductor/SummarizedExperiment#59 · 1 comment · Opened Oct 7, 2021
Add rownames check for cbind() Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

Bioconductor/SummarizedExperiment#53 · 1 reaction · Opened Jul 30, 2021
More informative error message for mismatching numbers of rows Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

Bioconductor/SummarizedExperiment#46 · Opened Oct 19, 2020
loading package taking too much memory Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Bioconductor/SummarizedExperiment#44 · 2 comments · Opened Aug 27, 2020
colData assignment should fail but does not Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Bioconductor/SummarizedExperiment#36 · 1 comment · Opened Feb 14, 2020
Slightly relaxing the rowData checks for cbind Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/SummarizedExperiment#33 · Opened Nov 28, 2019
Should `rowData` be merged with `mcols(gr)`? Open

question

Difficulty 5/5 Over a week Newbie friendliness 30/100

Bioconductor/SummarizedExperiment#30 · 2 comments · Opened Jul 25, 2019
derived RSE to SE coercion discards names Open

Bioconductor/SummarizedExperiment#29 · 15 comments · 1 assignee · Opened Jul 23, 2019
c() does not work on SummarizedExperiment Open

Bioconductor/SummarizedExperiment#27 · 1 comment · 2 reactions · 1 assignee · Opened Jul 18, 2019
SummarizedExperiment::cbind Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/SummarizedExperiment#23 · 3 comments · 1 reaction · Opened Jun 12, 2019
Implement an all.equal() method for SummarizedExperiment objects that performs a "deep comparison" Open

Bioconductor/SummarizedExperiment#22 · 1 assignee · Opened May 16, 2019
rowData rownames issue explored at BioC2018 Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/SummarizedExperiment#13 · 6 comments · 1 reaction · Opened Jul 26, 2018

Bioconductor/SummarizedExperiment

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