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hdf5array
•
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0
votes
3
replies
532
views
Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
4 months ago
Stefano Mangiola
▴ 40
3
votes
3
replies
1.0k
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
11 months ago
jacques.imbert
• 0
4
votes
6
replies
1.5k
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 12 months ago by
Akshay
• 0 • written 16 months ago by
Sarah
▴ 10
0
votes
2
replies
1.0k
views
Error in H5Fopen
HDF5Array
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
gabriele.favaretto
• 0
4
votes
3
replies
2.4k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array
SingleCellExperiment
DelayedArray
2.6 years ago • updated 2.5 years ago
merv
▴ 150
1
vote
1
reply
1.9k
views
Extract only dataframes from AnnData objects
rhdf5
HDF5Array
anndata
SingleCellExperiment
updated 2.6 years ago by
Peter Hickey
▴ 750 • written 2.6 years ago by
merv
▴ 150
5
votes
1
reply
3.6k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array
SingleCellExperiment
DelayedArray
2.6 years ago
merv
▴ 150
0
votes
0
replies
1.5k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
2.6 years ago
merv
▴ 150
4
votes
3
replies
1.4k
views
Problem opening hdf5 files previously created with HDF5Array functions
HDF5Array
updated 3.5 years ago by
Mike Smith
★ 6.6k • written 3.5 years ago by
eric.kern13
▴ 20
4
votes
13
replies
2.7k
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
updated 18 months ago by
Hervé Pagès
16k • written 3.5 years ago by
Koki
▴ 10
4
votes
3
replies
1.4k
views
Temporal directory setting for DelayedArray
HDF5Array
DelayedArray
3.7 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 3.8 years ago by
Hervé Pagès
16k • written 3.8 years ago by
Koki
▴ 10
3
votes
5
replies
1.8k
views
Block processing matrices of different dimensions with DelayedArray
HDF5Array
DelayedArray
updated 3.8 years ago by
Hervé Pagès
16k • written 3.8 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
3.8 years ago
Koki
▴ 10
9
votes
8
replies
2.0k
views
Processing time of blockApply and DelayedArray
DelayedArray
HDF5Array
updated 3.8 years ago by
Hervé Pagès
16k • written 3.9 years ago by
Pedro Baldoni
▴ 40
2
votes
4
replies
1.5k
views
`aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size aware?
HDF5Array
DelayedArray
3.9 years ago
Koki
▴ 10
1
vote
2
replies
1.4k
views
Error: C stack usage of HDF5Array
DelayedArray
HDF5Array
3.9 years ago
Koki
▴ 10
2
votes
6
replies
1.9k
views
"dim<-" against on-disk arrays
DelayedArray
TileDBArray
HDF5Array
updated 3.8 years ago by
Hervé Pagès
16k • written 4.0 years ago by
Koki
▴ 10
6
votes
6
replies
2.2k
views
Is it possible to create `HDF5Array` Delayed Arrays from HDF5 files hosted on S3?
TileDBArray
HDF5Array
MultiAssayExperiment
4.1 years ago
Thomas Sandmann
▴ 90
4
votes
2
replies
1.7k
views
HDF5Array Single cell experiment objects - can on-disk files change?
HDF5Array
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
sarah.williams1
▴ 40
1
vote
4
replies
2.3k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 6.6 years ago by
James W. MacDonald
68k • written 6.6 years ago by
Alexander Azarian
▴ 30
12
votes
15
replies
4.4k
views
error with HDF5Array
hdf5array
biocparallel
updated 6.9 years ago by
Mike Smith
★ 6.6k • written 6.9 years ago by
cath
▴ 30
4
votes
1
reply
3.0k
views
Using HDF5Array writeHDF5Array for a large dgCMatrix
HDF5Array
dgCMatrix
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
rubi
▴ 110
23 results • Page
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Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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