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HDF5Array
•
reset
0
votes
3
replies
506
views
Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
3 months ago
Stefano Mangiola
▴ 40
3
votes
3
replies
903
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
10 months ago
jacques.imbert
• 0
4
votes
6
replies
1.4k
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 11 months ago by
Akshay
• 0 • written 15 months ago by
Sarah
▴ 10
0
votes
2
replies
977
views
Error in H5Fopen
HDF5Array
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
gabriele.favaretto
• 0
4
votes
3
replies
2.3k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array
SingleCellExperiment
DelayedArray
2.5 years ago • updated 2.4 years ago
merv
▴ 150
1
vote
1
reply
1.8k
views
Extract only dataframes from AnnData objects
rhdf5
HDF5Array
anndata
SingleCellExperiment
updated 2.5 years ago by
Peter Hickey
▴ 750 • written 2.5 years ago by
merv
▴ 150
5
votes
1
reply
3.5k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array
SingleCellExperiment
DelayedArray
2.5 years ago
merv
▴ 150
0
votes
0
replies
1.5k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
2.5 years ago
merv
▴ 150
4
votes
3
replies
1.4k
views
Problem opening hdf5 files previously created with HDF5Array functions
HDF5Array
updated 3.4 years ago by
Mike Smith
★ 6.6k • written 3.4 years ago by
eric.kern13
▴ 20
4
votes
13
replies
2.6k
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
updated 17 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
3.6 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 3.7 years ago by
Hervé Pagès
16k • written 3.7 years ago by
Koki
▴ 10
3
votes
5
replies
1.7k
views
Block processing matrices of different dimensions with DelayedArray
HDF5Array
DelayedArray
updated 3.7 years ago by
Hervé Pagès
16k • written 3.7 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 • updated 3.7 years ago
Koki
▴ 10
9
votes
8
replies
1.9k
views
Processing time of blockApply and DelayedArray
DelayedArray
HDF5Array
updated 3.7 years ago by
Hervé Pagès
16k • written 3.8 years ago by
Pedro Baldoni
▴ 40
2
votes
4
replies
1.5k
views
`aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size aware?
HDF5Array
DelayedArray
3.8 years ago
Koki
▴ 10
1
vote
2
replies
1.4k
views
Error: C stack usage of HDF5Array
DelayedArray
HDF5Array
3.8 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 3.9 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
4.0 years ago
Thomas Sandmann
▴ 90
4
votes
2
replies
1.6k
views
HDF5Array Single cell experiment objects - can on-disk files change?
HDF5Array
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
sarah.williams1
▴ 40
1
vote
4
replies
2.3k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 6.5 years ago by
James W. MacDonald
68k • written 6.5 years ago by
Alexander Azarian
▴ 30
12
votes
15
replies
4.3k
views
error with HDF5Array
hdf5array
biocparallel
updated 6.8 years ago by
Mike Smith
★ 6.6k • written 6.8 years ago by
cath
▴ 30
4
votes
1
reply
2.9k
views
Using HDF5Array writeHDF5Array for a large dgCMatrix
HDF5Array
dgCMatrix
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
rubi
▴ 110
23 results • Page
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Replies
Comment: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression
by
Jane
• 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga
by
Jane
• 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output
by
Matthew McCormack
▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to
by
ATpoint
★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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