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BiocParallel
•
reset
1
vote
2
replies
89
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
2 days ago • updated 1 day ago
ATpoint
★ 4.0k
3
votes
3
replies
173
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
13 days ago • updated 8 days ago
jacques.imbert
• 0
0
votes
3
replies
411
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel
scran
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
qwang178
• 0
1
vote
4
replies
567
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
4 months ago
hayleyw
• 0
0
votes
2
replies
1.2k
views
Error: BiocParallel errors
xcms
msdata
BiocParallel
7 months ago
mavamay
• 0
1
vote
11
replies
1.5k
views
BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
BiocParallel
updated 11 months ago by
Martin Morgan
25k • written 11 months ago by
Michael Steinbaugh
▴ 90
0
votes
2
replies
1.1k
views
Usinig BiocParallel package in R with M1 MAC
RStudio
R
M1
BiocParallel
Mac
updated 15 months ago by
Christian Mertes
• 0 • written 17 months ago by
me.achleitner
• 0
0
votes
1
reply
748
views
Biocparallel Error "Error: BiocParallel errors element index: 1, 2, 3 first error: unable to find an inherited method for function ‘bpbackend’ fo…
R
OUTRIDER
BiocParallel
updated 15 months ago by
Christian Mertes
• 0 • written 17 months ago by
me.achleitner
• 0
1
vote
1
reply
663
views
Limit the number of nodes in DESeq2
DESeq2
BiocParallel
updated 18 months ago by
ATpoint
★ 4.0k • written 18 months ago by
Sebastian
▴ 10
0
votes
0
replies
1.0k
views
gseDo function issue
Biocpa
BiocParallel
18 months ago
meetdpanjwani1990
• 0
4
votes
13
replies
3.7k
views
BiocParallel error with ChIPQC
BiocManager
ChIPQC
RSamtools
BiocParallel
updated 15 months ago by
Rory Stark
★ 5.2k • written 22 months ago by
etiennedanis
• 0
2
votes
4
replies
1.0k
views
Load packages when using BatchtoolsParam
BatchtoolsParam
BiocParallel
2.1 years ago • updated 23 months ago
jianhai.zhang
• 0
3
votes
2
replies
1.2k
views
BiocParallel errors from muscat
BiocParallel
muscat
single-cell
2.1 years ago
tangming2005
▴ 190
1
vote
1
reply
760
views
Use MulticoreParam under BatchtoolsParam
BatchtoolsParam
MulticoreParam
BiocParallel
updated 2.1 years ago by
Martin Morgan
25k • written 2.1 years ago by
jianhai.zhang
• 0
1
vote
2
replies
2.6k
views
BiocParallel error when running DiffBind
BiocParallel
BiocPa
DiffBind
updated 2.1 years ago by
Martin Morgan
25k • written 2.2 years ago by
r.finn
▴ 10
0
votes
3
replies
713
views
How to get DESeq2 results in large count matix files?
DESeq2
BiocParallel
MulticoreParam
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
mathavanbioinfo
▴ 20
0
votes
0
replies
637
views
BiocParallel errors in XCMS peak-picking
BiocParallel
xcms
biocparallel
2.4 years ago
noerman
• 0
1
vote
5
replies
1.4k
views
slow bplapply?
BiocParallel
2.5 years ago • updated 16 months ago
Wu, Hao
▴ 20
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
2.5 years ago
enricoferrero
▴ 660
0
votes
4
replies
1.8k
views
DESeq2::DESeq(..., parallel = TRUE) fails if a partition has only genes with 0 counts across all samples
DESeq2
BiocParallel
2.7 years ago
Steffi Grote
▴ 10
2
votes
2
replies
1.3k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA
BPPARAM
scater
BiocParallel
runPCA
2.9 years ago
doliv071
• 0
0
votes
1
reply
1.1k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel
limma
variancePartition
3.0 years ago • updated 2.8 years ago
Junghoon
▴ 10
0
votes
1
reply
1.1k
views
Error while running variancePartition::dream()
variancePartition
limma
BiocParallel
3.0 years ago
Junghoon
▴ 10
0
votes
4
replies
1.1k
views
BiocParallel: bplapply invents data
BiocParallel
ShortRead
3.1 years ago
robmaz77
▴ 20
0
votes
0
replies
1.4k
views
BiocParallel errors with xcms
BiocParallel
xcms
3.1 years ago
Yuki
▴ 10
2
votes
2
replies
906
views
how to use biocParallel for large local variables?
BiocParallel
3.3 years ago
oyoung122
▴ 20
3
votes
3
replies
1.4k
views
first error: could not find function "readGAlignments" in BiocParallel
BiocParallel
3.3 years ago
Guandong Shang
▴ 40
1
vote
1
reply
1.4k
views
DiffBind error with background=TRUE in dba.normalize?
BiocParallel
DiffBind
parallel
updated 3.3 years ago by
Rory Stark
★ 5.2k • written 3.3 years ago by
Victor
• 0
0
votes
1
reply
849
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 3.3 years ago by
Matthias Lienhard
▴ 240 • written 3.3 years ago by
mbk0asis
• 0
3
votes
7
replies
2.1k
views
Which version of R to use for "HiCDCPlus" "HiC-DC+"
HiC-DC+
HiCDCPlus
BiocParallel
updated 3.2 years ago by
koushik
• 0 • written 3.4 years ago by
Tay
▴ 10
0
votes
0
replies
682
views
Job:
Two Fellowship Positions in Bioinformatics and Toxicology are avaiable immediately at US EPA
job
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
whduke
• 0
7
votes
4
replies
1.7k
views
How does BiocParallel export variables to threads?
BiocParallel
SnowParam
parallel
updated 3.8 years ago by
Martin Morgan
25k • written 3.8 years ago by
gabriel.hoffman
▴ 110
0
votes
6
replies
1.1k
views
BiocParallel with drake hangs
BiocParallel
4.2 years ago
biomiha
▴ 20
2
votes
2
replies
726
views
Number of MPI slaves in BiocParallel
BiocParallel
updated 4.2 years ago by
Martin Morgan
25k • written 4.2 years ago by
Homer
• 0
0
votes
2
replies
816
views
Run jobs asynchronously with BiocParellel
BiocParallel
future
batchtools
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
Qiang
▴ 80
0
votes
2
replies
1.0k
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2
DEXSeq
BioCParallel
updated 4.6 years ago by
Alejandro Reyes
★ 1.9k • written 4.6 years ago by
acciardo
• 0
1
vote
4
replies
2.0k
views
BiocParallel: What its the best way to pass large a dataset for parallel processing?
bioconductor
bplapply
bpiterate
iterator
BiocParallel
updated 4.8 years ago by
Martin Morgan
25k • written 4.8 years ago by
gabriel.hoffman
▴ 110
0
votes
1
reply
1.4k
views
ChIPQC BiocParallel errors
ChIPQC
ChIPQC error
BiocParallel
4.8 years ago
minervajunjun
• 0
2
votes
1
reply
1.9k
views
Rsubread installation problem
Rsubread
BiocParallel
updated 4.9 years ago by
Gordon Smyth
50k • written 4.9 years ago by
agustin.gonvi
▴ 20
2
votes
3
replies
1.4k
views
bplapply - only SerialParam or single worker Multicore working on R/macos 10.14
BiocParallel
mac
R
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
geo.vogler
▴ 10
0
votes
6
replies
1.6k
views
how to achieve reproducibility with BiocParallel regardless of number of threads and OS (set.seed is disallowed)
BiocParallel
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
luluchen
• 0
3
votes
6
replies
1.3k
views
nbinomLRT function all cores usage
deseq2
nbinomLRT
sample size
biocparallel
updated 5.5 years ago by
davide risso
▴ 950 • written 5.5 years ago by
mcalgaro93
• 0
2
votes
5
replies
2.5k
views
Issue with BiocParallel
purecn
biocparallel
5.5 years ago
milos-91
• 0
6
votes
8
replies
1.9k
views
BioParallel::BatchtoolsParam() - how to pass customized resource variables to batchtool's "slurm-simple" template using BatchtoolsParam()?
biocparallel
BatchtoolsParam
updated 5.5 years ago by
Mike Smith
★ 6.5k • written 5.5 years ago by
Chao-Jen Wong
▴ 40
4
votes
2
replies
915
views
bpaggregate with formula returns strange error message
biocparallel
bpaggregate
aggregate
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
maltethodberg
▴ 170
5
votes
6
replies
2.8k
views
BiocParallel: database disk image is malformed
biocparallel
databases
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
Paul Shannon
▴ 470
1
vote
1
reply
1.6k
views
Installing package BiocParallel failed
biocparallel
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 years ago by
Jiang, Mike
★ 1.3k
1
vote
5
replies
1.2k
views
Help using 'handler' function with bptry()
biocparallel
error handling
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 years ago by
Peter Hickey
▴ 740
12
votes
15
replies
3.4k
views
error with HDF5Array
hdf5array
biocparallel
updated 5.9 years ago by
Mike Smith
★ 6.5k • written 6.0 years ago by
cath
▴ 30
0
votes
1
reply
1.3k
views
Write gds in parallel
gds
SNPRelate
BiocParallel
updated 6.0 years ago by
zhengx
▴ 30 • written 6.0 years ago by
Vinicius Henrique da Silva
▴ 40
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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