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hdf5array
•
reset
2
votes
3
replies
382
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array
SingleCellExperiment
DelayedArray
6 months ago • updated 5 months ago
merv
▴ 60
1
vote
1
reply
335
views
Extract only dataframes from AnnData objects
rhdf5
HDF5Array
anndata
SingleCellExperiment
updated 6 months ago by
Peter Hickey
▴ 640 • written 6 months ago by
merv
▴ 60
1
vote
1
reply
451
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array
SingleCellExperiment
DelayedArray
6 months ago
merv
▴ 60
0
votes
0
replies
184
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
6 months ago
merv
▴ 60
4
votes
3
replies
537
views
Problem opening hdf5 files previously created with HDF5Array functions
HDF5Array
updated 17 months ago by
Mike Smith
★ 6.0k • written 17 months ago by
eric.kern13
▴ 20
1
vote
3
replies
636
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
18 months ago • updated 17 months ago
Koki
▴ 10
4
votes
3
replies
589
views
Temporal directory setting for DelayedArray
HDF5Array
DelayedArray
20 months ago
Koki
▴ 10
2
votes
3
replies
635
views
Generating a DelayedArray with a size greater than .Machine$integer.max
bit64
HDF5Array
DelayedArray
updated 21 months ago by
Hervé Pagès
16k • written 21 months ago by
Koki
▴ 10
3
votes
5
replies
758
views
Block processing matrices of different dimensions with DelayedArray
HDF5Array
DelayedArray
updated 21 months ago by
Hervé Pagès
16k • written 21 months ago by
Pedro Baldoni
▴ 30
0
votes
1
reply
466
views
How to incrementaly load the nzdata and nzindex from SparseArraySeed
TileDBArray
HDF5Array
DelayedArray
21 months ago
Koki
▴ 10
9
votes
8
replies
834
views
Processing time of blockApply and DelayedArray
DelayedArray
HDF5Array
updated 21 months ago by
Hervé Pagès
16k • written 22 months ago by
Pedro Baldoni
▴ 30
2
votes
4
replies
675
views
`aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size aware?
HDF5Array
DelayedArray
22 months ago
Koki
▴ 10
1
vote
2
replies
721
views
Error: C stack usage of HDF5Array
DelayedArray
HDF5Array
23 months ago
Koki
▴ 10
2
votes
6
replies
995
views
"dim<-" against on-disk arrays
DelayedArray
TileDBArray
HDF5Array
updated 22 months ago by
Hervé Pagès
16k • written 23 months ago by
Koki
▴ 10
6
votes
6
replies
1.0k
views
Is it possible to create `HDF5Array` Delayed Arrays from HDF5 files hosted on S3?
TileDBArray
HDF5Array
MultiAssayExperiment
2.1 years ago
Thomas Sandmann
▴ 80
4
votes
2
replies
923
views
HDF5Array Single cell experiment objects - can on-disk files change?
HDF5Array
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
sarah.williams1
▴ 40
1
vote
4
replies
1.3k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 4.6 years ago by
James W. MacDonald
62k • written 4.6 years ago by
Alexander Azarian
▴ 30
12
votes
15
replies
2.3k
views
error with HDF5Array
hdf5array
biocparallel
updated 4.8 years ago by
Mike Smith
★ 6.0k • written 4.9 years ago by
cath
▴ 30
4
votes
1
reply
1.5k
views
Using HDF5Array writeHDF5Array for a large dgCMatrix
HDF5Array
dgCMatrix
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
rubi
▴ 110
19 results • Page
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Comment: Time-course, comparison of two groups
by
boczniak767
▴ 720
As an exercise I've tried to analyze simpler but similar experiment. The data is from real experiment comparing wild type and mutant transc…
Answer: How to getting synonymous SNPs from BiomaRt before timing out?
by
James W. MacDonald
62k
Asking for multiple things at once will tend to blow out your results, as you will get every possible combination. ``` > options(timeou…
Comment: Definition of disease_subtype abbreviations
by
Lucas Schiffer
▴ 240
Hi Sehyun, I do not know myself and can only find one reference in the [template.csv](https://github.com/waldronlab/curatedMetagenomicDataC…
Answer: Are polynomial contrasts for a time factor possible in DESeq2?
by
ATpoint
★ 2.3k
As you can use a model.matrix() as input for the design you can use a great variety of models. A great read is this work from Ritchie/Smyth…
Comment: does anyone how to create rarefaction curves from a phyloseq object?
by
RMiller
• 0
I am not sure what you have tried, but the "vegan" library (package) has the ability to do rarefaction. So make sure to load `library("veg…
Votes
Are polynomial contrasts for a time factor possible in DESeq2?
Answer: How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_R
Comment: TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from va
A: Pathway analysis of differentially methylated CpGs
Comment: TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from va
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