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HDF5Array
•
reset
0
votes
3
replies
445
views
Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
6 weeks ago • updated 4 weeks ago
Stefano Mangiola
▴ 20
3
votes
3
replies
754
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
8 months ago
jacques.imbert
• 0
4
votes
6
replies
1.3k
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 9 months ago by
Akshay
• 0 • written 13 months ago by
Sarah
▴ 10
0
votes
2
replies
906
views
Error in H5Fopen
HDF5Array
updated 17 months ago by
James W. MacDonald
67k • written 17 months ago by
gabriele.favaretto
• 0
2
votes
3
replies
2.1k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array
SingleCellExperiment
DelayedArray
2.3 years ago
merv
▴ 140
1
vote
1
reply
1.7k
views
Extract only dataframes from AnnData objects
rhdf5
HDF5Array
anndata
SingleCellExperiment
updated 2.3 years ago by
Peter Hickey
▴ 740 • written 2.3 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
2.3 years ago
merv
▴ 140
0
votes
0
replies
1.4k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
2.3 years ago
merv
▴ 140
4
votes
3
replies
1.3k
views
Problem opening hdf5 files previously created with HDF5Array functions
HDF5Array
updated 3.2 years ago by
Mike Smith
★ 6.6k • written 3.2 years ago by
eric.kern13
▴ 20
4
votes
13
replies
2.4k
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 3.5 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
1.8k
views
Processing time of blockApply and DelayedArray
DelayedArray
HDF5Array
updated 3.6 years ago by
Hervé Pagès
16k • written 3.6 years ago by
Pedro Baldoni
▴ 40
2
votes
4
replies
1.3k
views
`aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size aware?
HDF5Array
DelayedArray
3.6 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 3.7 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 • updated 3.8 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 6.6 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
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Replies
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character
by
ATpoint
★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format
by
ControlF5
• 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open!
by
Alan Downey
• 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
by
O'Brien
• 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts
by
O'Brien
• 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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