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hdf5array
•
reset
0
votes
3
replies
493
views
Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
3 months ago • updated 12 weeks ago
Stefano Mangiola
▴ 20
3
votes
3
replies
877
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
965
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 16 months ago by
Hervé Pagès
16k • written 3.4 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
3.7 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 3.7 years ago by
Pedro Baldoni
▴ 40
2
votes
4
replies
1.4k
views
`aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size aware?
HDF5Array
DelayedArray
3.8 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 3.7 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
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
2.2k
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
4.2k
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
Answer: Plot title for PCA in DESeq2
by
ATpoint
★ 4.7k
The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
Comment: DESeq2 It is correct to use interaction term for patient variability?
by
Bradley
• 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Comment: Differential variance analysis - can i use deseq2
by
Michael Love
43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis
by
Gordon Smyth
52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA
by
pammelala304
• 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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