Bioconductor/SummarizedExperiment

Issues

• loading package taking too much memory

  #44 opened 4 years ago by spocks
  2

• Clarify withDimnames=FALSE in the documentation

  #79 opened 10 months ago by SamGG
  3

• Rows being removed from ASV table when building SummarizedExperiment

  #77 opened a year ago by yasminhilliam
  0

• Depreciated function calls in DelayedArray

  #76 opened a year ago by mingl1997
  4

• Warning and error message when using '$' operator on summarizedExperiment object

  #75 opened a year ago by DijkJel
  5

• Warning about dim, nrow and ncol deprecated methods.

  #74 opened a year ago by charles-plessy
  0

• colData Default in Constructor Inconsistency

  #73 opened a year ago by DarioS
  1

• metadata function is not exported as others

  #72 opened 2 years ago by hsiaoyi0504
  1

• Feature request: keep rownames(se) and rownames() of DataFrame nested in rowData(se) in sync

  #71 opened 2 years ago by kevinrue
  4

• Curious about how Rd manuals are generated

  #70 opened 2 years ago by mvfki
  3

• Add an `assaybind()` method

  #69 opened 2 years ago by multimeric
  0

• package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'SummarizedExperiment'

  #68 opened 2 years ago by bakaufman
  1

• Erroneous behaviour when colData is data.frame

  #67 opened 2 years ago by TuomasBorman
  0

• `combineCols` should keep names in metadata with `use.names=TRUE`

  #66 opened 2 years ago by LTLA
  0

• Remove all dimnames in `combine_assays_by` to avoid constructor check failures

  #65 opened 2 years ago by LTLA
  3

• Consider assayData DataFrame for assays

  #62 opened 2 years ago by jmw86069
  6

• `all.equal(x, y)` vs `all(x == y)`

  #64 opened 2 years ago by LiNk-NY
  3

• Constructor could check that assay is in matric format

  #63 opened 2 years ago by TuomasBorman
  2

• `combineCols()` and `combineRows()` not listed in 'Usage' section

  #61 opened 3 years ago by PeteHaitch
  4

• Enforce unique assay names

  #60 opened 3 years ago by hpages
  2

• Should the show() method for SummarizedExperiment objects suggest saveHDF5SummarizedExperiment()?

  #59 opened 3 years ago by hpages
  1

• Adding checkDimnames=FALSE to the SE constructor

  #57 opened 3 years ago by LTLA
  1

• subset fails when subsetting a SummarizedExperiment object with no samples

  #58 opened 3 years ago by kpagacz
  11

• Subsetting

  #55 opened 3 years ago by antagomir
  2

• assay<- is too pedantic when the dimensions are named

  #51 opened 3 years ago by LTLA
  2

• Constructor assigns wrong assay values to wrong samples and features

  #56 opened 3 years ago by TuomasBorman
  7

• Vignette Doesn't Specify Dimensionality Rules

  #52 opened 3 years ago by DarioS
  1

• Add rownames check for cbind()

  #53 opened 3 years ago by tavareshugo
  0

• Add a showAsCell method for SummarizedExperiment objects

  #50 opened 3 years ago by LTLA
  1

• Conversion to SingleCellExpriment object

  #49 opened 4 years ago by zhli12
  1

• fail to create `rbind` for SE-derived class due to the validity check

  #47 opened 4 years ago by fionarhuang
  2

• More informative error message for mismatching numbers of rows

  #46 opened 4 years ago by LTLA
  0

• “SimpleAssays” is not a defined class

  #42 opened 4 years ago by Georgy415
  2

• Coercion from SummarizedExperiment to ExpressionSet creates an unlocked environment

  #43 opened 4 years ago by tomsing1
  3

• Incorrect document page

  #41 opened 4 years ago by Jiefei-Wang
  2

• Improving the performance when calling assays accessor on a SummarizedExperiment object?

  #40 opened 4 years ago by Jiefei-Wang
  2

• derived RSE to SE coercion discards names

  #29 opened 5 years ago by LTLA
  15

• a = SimpleList(setNames(nm = list())); assays(SummarizedExperiment(a)) is no longer endomorphic

  #38 opened 5 years ago by mtmorgan
  6

• error object 'normalize_names_replacement_value' not found

  #37 opened 5 years ago by weibei43
  9

• SummarizedExperiment R package not allowing installation.

  #26 opened 5 years ago by joao1980
  8

• colnames-related concerns

  #35 opened 5 years ago by vjcitn
  5

• colData assignment should fail but does not

  #36 opened 5 years ago by vjcitn
  1

• Slightly relaxing the rowData checks for cbind

  #33 opened 5 years ago by LTLA
  0

• c() does not work on SummarizedExperiment

  #27 opened 5 years ago by lawremi
  1

• Build an assay element to work from my own normalized count matrix

  #32 opened 5 years ago by ramarquezo
  5

• seqinfo<-() fails when @rowData is a GRangesList

  #28 opened 5 years ago by lawremi
  2

• Extraction isn't working with ShallowSimpleListAssays on Bioc Devel 3.10

  #31 opened 5 years ago by mjsteinbaugh
  4

• Should `rowData` be merged with `mcols(gr)`?

  #30 opened 5 years ago by LiNk-NY
  2

• assayNames<- is reluctant to work

  #25 opened 5 years ago by LTLA
  5

• Why is SummarizedExperiment graphic not directly included in package?

  #24 opened 5 years ago by PeteHaitch
  4