waldronlab MultiAssayExperiment issues

waldronlab / MultiAssayExperiment

Bioconductor package for management of multi-assay data

https://waldronlab.io/MultiAssayExperiment/

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issues

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Combining multiple (different modality) sce objects to MAE

#332 JHYSiu opened 1 week ago
1
Issue with longFormat and numeric row names

#331 lgatto closed 4 months ago
1
improve error message when assigning data.frame to colData

#330 drighelli closed 5 months ago
1
bug fix: use reshape2::melt instead of stats::reshape

#329 LiNk-NY closed 6 months ago
0
use markdown in docs

#328 LiNk-NY closed 6 months ago
0
1.27.1 constructor breaks with out-of-order sample mapping columns

#326 LTLA closed 1 year ago
1
Error in h5checktype(). The provided H5Identifier is not a dataset identifier.

#325 JHYSiu opened 1 year ago
6
`MultiAssayExperiment()` allows construction of an empty `sampleMap` with non-empty experiments

#324 LTLA closed 1 year ago
2
Assigning to metadata causes endless duplication of `drop.experiments`

#323 LTLA closed 1 year ago
2
Error subscript contains invalid rownames (guess when one experiment has 0 rows)

#322 danielinteractive closed 1 year ago
2
Show Method Breaks if R Package tictoc is Loaded

#321 DarioS closed 1 year ago
7
Subsequently Reordering a Renamed Experiment List Causes All Samples to be Dropped

#320 DarioS closed 1 year ago
2
Bracket replacement method for a single assay

#319 LiNk-NY closed 1 year ago
1
Error = All sample identifiers in the assays must be unique

#318 jfertaj closed 1 year ago
2
Assay levels are dropped in sampleMap after subsetByColData

#317 cvanderaa closed 2 years ago
2
Bug in subsetByColData()

#316 cvanderaa closed 2 years ago
2
Error when combining 2 MAE objects that have 1 column in colData

#315 cvanderaa closed 2 years ago
2
Questions about `.sampleMapFromData()`

#314 cvanderaa closed 2 years ago
1
wideFormat Introduces Missing Data and Changes Data Dimensions

#312 DarioS closed 2 years ago
6
issue using `upsetSamples`?

#311 bblodfon closed 2 years ago
1
chr/start/stop nomenclature disagreements between maftools and GRanges

#308 grindhej closed 2 years ago
1
MultiAssayExperimentToMAF grepl bug

#307 grindhej closed 2 years ago
0
Fix new("MultiAssayExperiment")

#306 hpages closed 2 years ago
1
Implement "deep" update of MultiAssayExperiment objects

#305 hpages closed 2 years ago
0
`na.rm` argument in `subsetByColData`

#304 gogonzo closed 1 year ago
4
Changes in subsetByColData between in 3.14

#303 gogonzo closed 3 years ago
6
Unexpected behavior after recursive call to `subsetByColData`

#302 cvanderaa closed 3 years ago
3
getWithColData: optionalize "harmonizing input" msg

#301 bhagwataditya closed 3 years ago
0
`getWithColData` fails when experiment has 0 rows or columns

#300 danielinteractive closed 3 years ago
2
Harmonization makes unnecessary copies of large datasets

#299 LTLA closed 3 years ago
1
Update documentation of wideFormat/longFormat args

#298 LiNk-NY closed 3 years ago
0
optimization of .harmonize

#297 cvanderaa closed 3 years ago
5
support saveHDF5MultiAssayExperiment with HDF5Array

#296 LiNk-NY closed 3 years ago
10
mae2maf

#295 PoisonAlien closed 3 years ago
1
Tiny detail: warning when subsetting all assays

#294 cvanderaa closed 3 years ago
2
Maf fix

#293 PoisonAlien closed 3 years ago
2
metadata items names change in 1.17.6

#292 mcjmigdal closed 3 years ago
2
All data dropped unless sampleMap provided

#291 lwaldron closed 3 years ago
1
Things I don't like about harmonization during subsetting

#290 LTLA closed 3 years ago
16
Harmonization should be more noisy and complaining (or better yet, an error)

#289 LTLA closed 3 years ago
12
Infer MAE-level colData from sampleMap when the former is not supplied

#287 LTLA closed 3 years ago
2
extend `longFormat` with to include rowData

#284 lgatto closed 4 years ago
2
Linear subsetting of an ExperimentList object is broken in MultiAssayExperiment 1.15.7

#283 hpages closed 4 years ago
4
*Format converts character assay data to factor

#282 jonocarroll closed 4 years ago
1
Expand documentation of setters and getters

#281 llrs closed 4 years ago
2
Use `tidyr::pivot_wider` in `wideFormat`

#280 LiNk-NY closed 4 years ago
1
getWithColData colnames

#279 mherberg closed 4 years ago
4
wideFormat() on SummarizedExperiment

#278 mherberg closed 4 years ago
1
Error in proxy[i, ..., drop = FALSE] : incorrect number of dimensions

#277 swvanderlaan closed 4 years ago
4
Error when subsetting features from a `SingleCellExperiment` object from `experiments(x)`

#276 cvanderaa closed 4 years ago
9