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hdf5array
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0
votes
3
replies
562
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Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
5 months ago
Stefano Mangiola
▴ 40
3
votes
3
replies
1.1k
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
12 months ago
jacques.imbert
• 0
4
votes
6
replies
1.5k
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 13 months ago by
Akshay
• 0 • written 17 months ago by
Sarah
▴ 10
0
votes
2
replies
1.1k
views
Error in H5Fopen
HDF5Array
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
gabriele.favaretto
• 0
4
votes
3
replies
2.5k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array
SingleCellExperiment
DelayedArray
2.6 years ago
merv
▴ 150
1
vote
1
reply
2.0k
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
3.7k
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
1.6k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
2.6 years ago
merv
▴ 150
4
votes
3
replies
1.5k
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 19 months ago by
Hervé Pagès
16k • written 3.6 years ago by
Koki
▴ 10
4
votes
3
replies
1.4k
views
Temporal directory setting for DelayedArray
HDF5Array
DelayedArray
3.8 years ago
Koki
▴ 10
2
votes
3
replies
1.5k
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 3.9 years ago by
Koki
▴ 10
3
votes
5
replies
1.8k
views
Block processing matrices of different dimensions with DelayedArray
HDF5Array
DelayedArray
updated 3.9 years ago by
Hervé Pagès
16k • written 3.9 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
3.9 years ago
Koki
▴ 10
9
votes
8
replies
2.0k
views
Processing time of blockApply and DelayedArray
DelayedArray
HDF5Array
updated 3.9 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
4.0 years ago • updated 3.9 years ago
Koki
▴ 10
1
vote
2
replies
1.4k
views
Error: C stack usage of HDF5Array
DelayedArray
HDF5Array
4.0 years ago
Koki
▴ 10
2
votes
6
replies
1.9k
views
"dim<-" against on-disk arrays
DelayedArray
TileDBArray
HDF5Array
updated 3.9 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
4.2 years ago
Thomas Sandmann
▴ 90
4
votes
2
replies
1.7k
views
HDF5Array Single cell experiment objects - can on-disk files change?
HDF5Array
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
sarah.williams1
▴ 40
1
vote
4
replies
2.4k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
Alexander Azarian
▴ 30
12
votes
15
replies
4.5k
views
error with HDF5Array
hdf5array
biocparallel
updated 6.9 years ago by
Mike Smith
★ 6.6k • written 7.0 years ago by
cath
▴ 30
4
votes
1
reply
3.0k
views
Using HDF5Array writeHDF5Array for a large dgCMatrix
HDF5Array
dgCMatrix
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
rubi
▴ 110
23 results • Page
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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