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HDF5Array
•
reset
2
votes
3
replies
299
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array
SingleCellExperiment
DelayedArray
4 months ago
merv
▴ 60
1
vote
1
reply
250
views
Extract only dataframes from AnnData objects
rhdf5
HDF5Array
anndata
SingleCellExperiment
updated 5 months ago by
Peter Hickey
▴ 630 • written 5 months ago by
merv
▴ 60
1
vote
1
reply
295
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array
SingleCellExperiment
DelayedArray
5 months ago
merv
▴ 60
0
votes
0
replies
146
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
5 months ago
merv
▴ 60
4
votes
3
replies
488
views
Problem opening hdf5 files previously created with HDF5Array functions
HDF5Array
updated 15 months ago by
Mike Smith
★ 5.9k • written 15 months ago by
eric.kern13
▴ 20
1
vote
3
replies
592
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
16 months ago
Koki
▴ 10
4
votes
3
replies
548
views
Temporal directory setting for DelayedArray
HDF5Array
DelayedArray
19 months ago
Koki
▴ 10
2
votes
3
replies
590
views
Generating a DelayedArray with a size greater than .Machine$integer.max
bit64
HDF5Array
DelayedArray
updated 19 months ago by
Hervé Pagès
16k • written 20 months ago by
Koki
▴ 10
3
votes
5
replies
708
views
Block processing matrices of different dimensions with DelayedArray
HDF5Array
DelayedArray
updated 20 months ago by
Hervé Pagès
16k • written 20 months ago by
Pedro Baldoni
▴ 20
0
votes
1
reply
388
views
How to incrementaly load the nzdata and nzindex from SparseArraySeed
TileDBArray
HDF5Array
DelayedArray
20 months ago
Koki
▴ 10
9
votes
8
replies
775
views
Processing time of blockApply and DelayedArray
DelayedArray
HDF5Array
updated 20 months ago by
Hervé Pagès
16k • written 20 months ago by
Pedro Baldoni
▴ 20
2
votes
4
replies
627
views
`aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size aware?
HDF5Array
DelayedArray
21 months ago • updated 20 months ago
Koki
▴ 10
1
vote
2
replies
684
views
Error: C stack usage of HDF5Array
DelayedArray
HDF5Array
21 months ago
Koki
▴ 10
2
votes
6
replies
937
views
"dim<-" against on-disk arrays
DelayedArray
TileDBArray
HDF5Array
updated 20 months ago by
Hervé Pagès
16k • written 21 months ago by
Koki
▴ 10
6
votes
6
replies
953
views
Is it possible to create `HDF5Array` Delayed Arrays from HDF5 files hosted on S3?
TileDBArray
HDF5Array
MultiAssayExperiment
23 months ago
Thomas Sandmann
▴ 80
4
votes
2
replies
883
views
HDF5Array Single cell experiment objects - can on-disk files change?
HDF5Array
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
sarah.williams1
▴ 40
1
vote
4
replies
1.2k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 4.5 years ago by
James W. MacDonald
62k • written 4.5 years ago by
Alexander Azarian
▴ 30
12
votes
15
replies
2.2k
views
error with HDF5Array
hdf5array
biocparallel
updated 4.7 years ago by
Mike Smith
★ 5.9k • written 4.8 years ago by
cath
▴ 30
4
votes
1
reply
1.5k
views
Using HDF5Array writeHDF5Array for a large dgCMatrix
HDF5Array
dgCMatrix
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
rubi
▴ 110
19 results • Page
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Answer: struggling to create a heatmap
by
ATpoint
★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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