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hdf5array
•
reset
0
votes
3
replies
878
views
Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
15 months ago • updated 14 months ago
Stefano Mangiola
▴ 40
3
votes
3
replies
2.0k
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
22 months ago
jacques.imbert
• 0
4
votes
6
replies
2.1k
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 23 months ago by
Akshay
• 0 • written 2.2 years ago by
Sarah
▴ 10
0
votes
2
replies
1.3k
views
Error in H5Fopen
HDF5Array
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
gabriele.favaretto
• 0
4
votes
3
replies
3.0k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array
SingleCellExperiment
DelayedArray
3.4 years ago
merv
▴ 150
1
vote
1
reply
2.7k
views
Extract only dataframes from AnnData objects
rhdf5
HDF5Array
anndata
SingleCellExperiment
updated 3.4 years ago by
Peter Hickey
▴ 760 • written 3.4 years ago by
merv
▴ 150
5
votes
1
reply
4.2k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array
SingleCellExperiment
DelayedArray
3.5 years ago
merv
▴ 150
0
votes
0
replies
2.1k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
3.5 years ago
merv
▴ 150
4
votes
3
replies
1.8k
views
Problem opening hdf5 files previously created with HDF5Array functions
HDF5Array
updated 4.3 years ago by
Mike Smith
★ 6.6k • written 4.3 years ago by
eric.kern13
▴ 20
4
votes
13
replies
3.5k
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
updated 2.4 years ago by
Hervé Pagès
16k • written 4.4 years ago by
Koki
▴ 10
4
votes
3
replies
1.7k
views
Temporal directory setting for DelayedArray
HDF5Array
DelayedArray
4.6 years ago
Koki
▴ 10
2
votes
3
replies
1.8k
views
Generating a DelayedArray with a size greater than .Machine$integer.max
bit64
HDF5Array
DelayedArray
updated 4.6 years ago by
Hervé Pagès
16k • written 4.7 years ago by
Koki
▴ 10
3
votes
5
replies
2.3k
views
Block processing matrices of different dimensions with DelayedArray
HDF5Array
DelayedArray
updated 4.7 years ago by
Hervé Pagès
16k • written 4.7 years ago by
Pedro Baldoni
▴ 40
0
votes
1
reply
1.3k
views
How to incrementaly load the nzdata and nzindex from SparseArraySeed
TileDBArray
HDF5Array
DelayedArray
4.7 years ago
Koki
▴ 10
9
votes
8
replies
2.5k
views
Processing time of blockApply and DelayedArray
DelayedArray
HDF5Array
updated 4.7 years ago by
Hervé Pagès
16k • written 4.7 years ago by
Pedro Baldoni
▴ 40
2
votes
4
replies
1.8k
views
`aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size aware?
HDF5Array
DelayedArray
4.8 years ago • updated 4.7 years ago
Koki
▴ 10
1
vote
2
replies
1.7k
views
Error: C stack usage of HDF5Array
DelayedArray
HDF5Array
4.8 years ago
Koki
▴ 10
2
votes
6
replies
2.3k
views
"dim<-" against on-disk arrays
DelayedArray
TileDBArray
HDF5Array
updated 4.7 years ago by
Hervé Pagès
16k • written 4.8 years ago by
Koki
▴ 10
6
votes
6
replies
2.8k
views
Is it possible to create `HDF5Array` Delayed Arrays from HDF5 files hosted on S3?
TileDBArray
HDF5Array
MultiAssayExperiment
5.0 years ago
Thomas Sandmann
▴ 90
4
votes
2
replies
2.0k
views
HDF5Array Single cell experiment objects - can on-disk files change?
HDF5Array
updated 7.0 years ago by
Aaron Lun
★ 29k • written 7.0 years ago by
sarah.williams1
▴ 40
1
vote
4
replies
2.7k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 7.5 years ago by
James W. MacDonald
68k • written 7.5 years ago by
Alexander Azarian
▴ 30
12
votes
15
replies
5.1k
views
error with HDF5Array
hdf5array
biocparallel
updated 7.7 years ago by
Mike Smith
★ 6.6k • written 7.8 years ago by
cath
▴ 30
4
votes
1
reply
3.9k
views
Using HDF5Array writeHDF5Array for a large dgCMatrix
HDF5Array
dgCMatrix
updated 7.9 years ago by
Aaron Lun
★ 29k • written 7.9 years ago by
rubi
▴ 110
23 results • Page
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Comment: Which preprocessing steps are needed before running limpa?
by
miro165sabo
• 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
by
Gordon Smyth
53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Korneel
• 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics
by
yesquokkan
• 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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