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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
922
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
Comment: How to sort negative log2FC or FC in RNAseq for GSEA?
by
alserg
▴ 280
`NES > 0` means that your gene set has more genes with positive logFC/stat. In your case these genes should be up in Subset1. However, if y…
Answer: affymetrix
by
James W. MacDonald
67k
When posting it helps to think about the people you are asking for help. Your post is hidden within the dummy text that comes up when you i…
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: 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…
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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Martin Morgan
25k
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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
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