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hdf5array
•
reset
0
votes
3
replies
467
views
Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
10 weeks ago • updated 8 weeks ago
Stefano Mangiola
▴ 20
3
votes
3
replies
799
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
9 months ago
jacques.imbert
• 0
4
votes
6
replies
1.3k
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 10 months ago by
Akshay
• 0 • written 14 months ago by
Sarah
▴ 10
0
votes
2
replies
921
views
Error in H5Fopen
HDF5Array
updated 18 months ago by
James W. MacDonald
67k • written 18 months ago by
gabriele.favaretto
• 0
2
votes
3
replies
2.2k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array
SingleCellExperiment
DelayedArray
2.4 years ago • updated 2.3 years ago
merv
▴ 140
1
vote
1
reply
1.7k
views
Extract only dataframes from AnnData objects
rhdf5
HDF5Array
anndata
SingleCellExperiment
updated 2.4 years ago by
Peter Hickey
▴ 750 • written 2.4 years ago by
merv
▴ 140
5
votes
1
reply
3.4k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array
SingleCellExperiment
DelayedArray
2.4 years ago
merv
▴ 140
0
votes
0
replies
1.4k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
2.4 years ago
merv
▴ 140
4
votes
3
replies
1.3k
views
Problem opening hdf5 files previously created with HDF5Array functions
HDF5Array
updated 3.3 years ago by
Mike Smith
★ 6.6k • written 3.3 years ago by
eric.kern13
▴ 20
4
votes
13
replies
2.5k
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
updated 15 months ago by
Hervé Pagès
16k • written 3.3 years ago by
Koki
▴ 10
4
votes
3
replies
1.3k
views
Temporal directory setting for DelayedArray
HDF5Array
DelayedArray
3.5 years ago
Koki
▴ 10
2
votes
3
replies
1.4k
views
Generating a DelayedArray with a size greater than .Machine$integer.max
bit64
HDF5Array
DelayedArray
updated 3.6 years ago by
Hervé Pagès
16k • written 3.6 years ago by
Koki
▴ 10
3
votes
5
replies
1.6k
views
Block processing matrices of different dimensions with DelayedArray
HDF5Array
DelayedArray
updated 3.6 years ago by
Hervé Pagès
16k • written 3.6 years ago by
Pedro Baldoni
▴ 40
0
votes
1
reply
1.1k
views
How to incrementaly load the nzdata and nzindex from SparseArraySeed
TileDBArray
HDF5Array
DelayedArray
3.6 years ago
Koki
▴ 10
9
votes
8
replies
1.9k
views
Processing time of blockApply and DelayedArray
DelayedArray
HDF5Array
updated 3.6 years ago by
Hervé Pagès
16k • written 3.7 years ago by
Pedro Baldoni
▴ 40
2
votes
4
replies
1.4k
views
`aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size aware?
HDF5Array
DelayedArray
3.7 years ago
Koki
▴ 10
1
vote
2
replies
1.3k
views
Error: C stack usage of HDF5Array
DelayedArray
HDF5Array
3.7 years ago
Koki
▴ 10
2
votes
6
replies
1.8k
views
"dim<-" against on-disk arrays
DelayedArray
TileDBArray
HDF5Array
updated 3.6 years ago by
Hervé Pagès
16k • written 3.8 years ago by
Koki
▴ 10
6
votes
6
replies
2.1k
views
Is it possible to create `HDF5Array` Delayed Arrays from HDF5 files hosted on S3?
TileDBArray
HDF5Array
MultiAssayExperiment
3.9 years ago
Thomas Sandmann
▴ 90
4
votes
2
replies
1.6k
views
HDF5Array Single cell experiment objects - can on-disk files change?
HDF5Array
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
sarah.williams1
▴ 40
1
vote
4
replies
2.2k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 6.4 years ago by
James W. MacDonald
67k • written 6.4 years ago by
Alexander Azarian
▴ 30
12
votes
15
replies
4.1k
views
error with HDF5Array
hdf5array
biocparallel
updated 6.7 years ago by
Mike Smith
★ 6.6k • written 6.7 years ago by
cath
▴ 30
4
votes
1
reply
2.8k
views
Using HDF5Array writeHDF5Array for a large dgCMatrix
HDF5Array
dgCMatrix
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
rubi
▴ 110
23 results • Page
1 of 1
Recent ...
Replies
Answer: Problems with GSEA
by
Guido Hooiveld
★ 4.1k
The error `Duplicate values in names(stats) not allowed` (from `fgsea` that is used under the hood) shows that the input is not unique; in …
Answer: Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
by
ja.garcia
• 0
It has been fixed by the Rbowtie2 maintainers in version 2.12.2. Thank you for the quick fix!
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
Amora
• 0
You did a great job giving an overview.....[slope][1] better than the bioconductor group! [1]: https://slopeio.org
Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression?
by
Peter Hickey
▴ 750
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Votes
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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Guido Hooiveld
★ 4.1k
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Joseph Fass
▴ 70
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Peter Hickey
▴ 750
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Gordon Smyth
52k
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Dario Strbenac
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