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BiocParallel
•
reset
1
vote
2
replies
177
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
25 days ago • updated 24 days ago
ATpoint
★ 4.1k
3
votes
3
replies
246
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 4 weeks ago
jacques.imbert
• 0
0
votes
3
replies
475
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel
scran
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
qwang178
• 0
1
vote
4
replies
676
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
5 months ago
hayleyw
• 0
0
votes
2
replies
1.3k
views
Error: BiocParallel errors
xcms
msdata
BiocParallel
8 months ago
mavamay
• 0
1
vote
11
replies
1.6k
views
BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
BiocParallel
updated 12 months ago by
Martin Morgan
25k • written 12 months ago by
Michael Steinbaugh
▴ 90
0
votes
2
replies
1.2k
views
Usinig BiocParallel package in R with M1 MAC
RStudio
R
M1
BiocParallel
Mac
updated 16 months ago by
Christian Mertes
• 0 • written 18 months ago by
me.achleitner
• 0
0
votes
1
reply
786
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 16 months ago by
Christian Mertes
• 0 • written 18 months ago by
me.achleitner
• 0
1
vote
1
reply
686
views
Limit the number of nodes in DESeq2
DESeq2
BiocParallel
updated 18 months ago by
ATpoint
★ 4.1k • written 18 months ago by
Sebastian
▴ 10
0
votes
0
replies
1.1k
views
gseDo function issue
Biocpa
BiocParallel
19 months ago
meetdpanjwani1990
• 0
4
votes
13
replies
3.8k
views
BiocParallel error with ChIPQC
BiocManager
ChIPQC
RSamtools
BiocParallel
updated 16 months ago by
Rory Stark
★ 5.2k • written 23 months ago by
etiennedanis
• 0
1
vote
2
replies
2.7k
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
1
vote
1
reply
780
views
Use MulticoreParam under BatchtoolsParam
BatchtoolsParam
MulticoreParam
BiocParallel
updated 2.2 years ago by
Martin Morgan
25k • written 2.2 years ago by
jianhai.zhang
• 0
2
votes
4
replies
1.1k
views
Load packages when using BatchtoolsParam
BatchtoolsParam
BiocParallel
2.2 years ago • updated 2.0 years ago
jianhai.zhang
• 0
3
votes
2
replies
1.2k
views
BiocParallel errors from muscat
BiocParallel
muscat
single-cell
2.2 years ago
tangming2005
▴ 190
0
votes
3
replies
750
views
How to get DESeq2 results in large count matix files?
DESeq2
BiocParallel
MulticoreParam
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
mathavanbioinfo
▴ 20
0
votes
0
replies
653
views
BiocParallel errors in XCMS peak-picking
BiocParallel
xcms
biocparallel
2.5 years ago
noerman
• 0
1
vote
5
replies
1.4k
views
slow bplapply?
BiocParallel
2.5 years ago • updated 17 months ago
Wu, Hao
▴ 20
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
2.6 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
2.8 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
1.2k
views
Error while running variancePartition::dream()
variancePartition
limma
BiocParallel
3.1 years ago
Junghoon
▴ 10
0
votes
1
reply
1.1k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel
limma
variancePartition
3.1 years ago • updated 2.9 years ago
Junghoon
▴ 10
0
votes
4
replies
1.1k
views
BiocParallel: bplapply invents data
BiocParallel
ShortRead
3.2 years ago
robmaz77
▴ 20
0
votes
0
replies
1.4k
views
BiocParallel errors with xcms
BiocParallel
xcms
3.2 years ago
Yuki
▴ 10
2
votes
2
replies
928
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
3.4 years ago
Guandong Shang
▴ 40
1
vote
1
reply
1.4k
views
DiffBind error with background=TRUE in dba.normalize?
BiocParallel
DiffBind
parallel
updated 3.4 years ago by
Rory Stark
★ 5.2k • written 3.4 years ago by
Victor
• 0
0
votes
1
reply
862
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 3.4 years ago by
Matthias Lienhard
▴ 240 • written 3.4 years ago by
mbk0asis
• 0
3
votes
7
replies
2.2k
views
Which version of R to use for "HiCDCPlus" "HiC-DC+"
HiC-DC+
HiCDCPlus
BiocParallel
updated 3.2 years ago by
koushik
• 0 • written 3.5 years ago by
Tay
▴ 10
0
votes
0
replies
699
views
Job:
Two Fellowship Positions in Bioinformatics and Toxicology are avaiable immediately at US EPA
job
updated 3.5 years ago by
Michael Love
42k • 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 3.9 years ago by
Martin Morgan
25k • written 3.9 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
756
views
Number of MPI slaves in BiocParallel
BiocParallel
updated 4.3 years ago by
Martin Morgan
25k • written 4.3 years ago by
Homer
• 0
0
votes
2
replies
838
views
Run jobs asynchronously with BiocParellel
BiocParallel
future
batchtools
updated 4.6 years ago by
Martin Morgan
25k • written 4.6 years ago by
Qiang
▴ 80
0
votes
2
replies
1.1k
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2
DEXSeq
BioCParallel
updated 4.7 years ago by
Alejandro Reyes
★ 1.9k • written 4.7 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
1.5k
views
ChIPQC BiocParallel errors
ChIPQC
ChIPQC error
BiocParallel
4.9 years ago
minervajunjun
• 0
2
votes
1
reply
2.0k
views
Rsubread installation problem
Rsubread
BiocParallel
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 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 5.2 years ago by
Martin Morgan
25k • written 5.2 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 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
luluchen
• 0
3
votes
6
replies
1.3k
views
nbinomLRT function all cores usage
deseq2
nbinomLRT
sample size
biocparallel
updated 5.6 years ago by
davide risso
▴ 950 • written 5.6 years ago by
mcalgaro93
• 0
2
votes
5
replies
2.6k
views
Issue with BiocParallel
purecn
biocparallel
5.6 years ago
milos-91
• 0
6
votes
8
replies
2.0k
views
BioParallel::BatchtoolsParam() - how to pass customized resource variables to batchtool's "slurm-simple" template using BatchtoolsParam()?
biocparallel
BatchtoolsParam
updated 5.6 years ago by
Mike Smith
★ 6.5k • written 5.6 years ago by
Chao-Jen Wong
▴ 40
4
votes
2
replies
935
views
bpaggregate with formula returns strange error message
biocparallel
bpaggregate
aggregate
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 years ago by
maltethodberg
▴ 180
5
votes
6
replies
2.9k
views
BiocParallel: database disk image is malformed
biocparallel
databases
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 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
1.3k
views
Help using 'handler' function with bptry()
biocparallel
error handling
updated 6.0 years ago by
Martin Morgan
25k • written 6.0 years ago by
Peter Hickey
▴ 740
12
votes
15
replies
3.5k
views
error with HDF5Array
hdf5array
biocparallel
updated 6.0 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 6.1 years ago by
zhengx
▴ 30 • written 6.1 years ago by
Vinicius Henrique da Silva
▴ 40
50 results • Page
1 of 1
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Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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