Showing : BioCParallel • reset
12
votes
11
replies
4.2k
views
Memory usage for bplapply -- is the entire environment copied over to each worker thread?
bplapply biocparallel deseq2
updated 8.8 years ago by ★ 6.8k • written 8.8 years ago by ▴ 40
12
votes
15
replies
3.4k
views
error with HDF5Array
hdf5array biocparallel
updated 5.9 years ago by ★ 6.5k • written 6.0 years ago by ▴ 30
7
votes
4
replies
1.7k
views
How does BiocParallel export variables to threads?
BiocParallel SnowParam parallel
updated 3.8 years ago by 25k • written 3.8 years ago by ▴ 110
6
votes
1
reply
3.9k
views
Tutorial: Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
rnaseq biocparallel workflows sra Tutorial
8.8 years ago Sean Davis 21k
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 ★ 6.5k • written 5.5 years ago by ▴ 40
5
votes
5
replies
1.6k
views
BiocParallel: messages shown only when processes finished
biocparallel
updated 6.9 years ago by 25k • written 6.9 years ago by ★ 2.0k
5
votes
5
replies
2.1k
views
SGE backend on Bioc AMI with Starcluster not recognising CPUs
ami starcluster biocparallel sge AWS
8.6 years ago n.huckle ▴ 30
5
votes
6
replies
2.8k
views
BiocParallel: database disk image is malformed
biocparallel databases
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 470
5
votes
2
replies
1.4k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
7.8 years ago • updated 7.5 years ago Jurat Shahidin ▴ 80
4
votes
5
replies
4.7k
views
BiocParallel on Windows : cannot find my functions when using SnowParam
BiocParallel SnowParam
updated 7.2 years ago by 25k • written 7.2 years ago by ▴ 60
4
votes
2
replies
915
views
bpaggregate with formula returns strange error message
biocparallel bpaggregate aggregate
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 170
4
votes
4
replies
1.4k
views
Load balancing using BiocParallel
biocparallel
8.3 years ago t.kuilman ▴ 170
4
votes
13
replies
3.7k
views
BiocParallel error with ChIPQC
BiocManager ChIPQC RSamtools BiocParallel
updated 15 months ago by ★ 5.2k • written 22 months ago by • 0
4
votes
3
replies
1.8k
views
BiocParallel: object export issue
BiocParallel DOSE
updated 7.5 years ago by 25k • written 7.5 years ago by ★ 3.9k
4
votes
1
reply
1.3k
views
Parallel Join Excessively Slow
biocparallel curatedmetagenomicdata parallel dplyr
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 240
4
votes
7
replies
6.3k
views
BiocParallel/scater warning after move to R 3.4.0
biocparallel scater
updated 6.8 years ago by ▴ 40 • written 7.0 years ago by • 0
4
votes
5
replies
1.3k
views
parRapply in BiocParallel ?
biocparallel variantannotation
updated 7.9 years ago by ★ 11k • written 7.9 years ago by ▴ 350
3
votes
6
replies
1.3k
views
nbinomLRT function all cores usage
deseq2 nbinomLRT sample size biocparallel
updated 5.5 years ago by ▴ 950 • written 5.5 years ago by • 0
3
votes
1
reply
828
views
passing submitJobs parameters from BatchJobsParam
biocparallel
updated 8.2 years ago by 25k • written 8.2 years ago by ★ 1.9k
3
votes
4
replies
1.1k
views
bplapply stalling upon error with large data objects
biocparallel bplapply multicore
updated 7.7 years ago by 25k • written 7.7 years ago by ★ 28k
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
3
votes
2
replies
1.2k
views
BiocParallel errors from muscat
BiocParallel muscat single-cell
2.1 years ago tangming2005 ▴ 190
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
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 • 0 • written 3.4 years ago by ▴ 10
3
votes
3
replies
1.4k
views
first error: could not find function "readGAlignments" in BiocParallel
BiocParallel
3.3 years ago Guandong Shang ▴ 40
3
votes
3
replies
1.6k
views
BiocParallel: zombie processes on FORK cluster
biocparallel parallel
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 240
3
votes
3
replies
1.1k
views
Parallel reading of Vcfs using VcfStack/RangedVcfStack
GenomicFiles BiocParallel
updated 6.8 years ago by 3.8k • written 6.9 years ago by ▴ 20
3
votes
2
replies
1.0k
views
Getting data/objects to workers in bplapply inside a function
biocparallel
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 190
2
votes
7
replies
2.7k
views
DESeq(): Forking of R Process even though parallel=FALSE
DESeq2 biocparallel
updated 7.6 years ago by 41k • written 7.6 years ago by • 0
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 25k • written 5.1 years ago by ▴ 10
2
votes
1
reply
1.9k
views
Rsubread installation problem
Rsubread BiocParallel
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 20
2
votes
10
replies
2.1k
views
Correct way to load a package inside bplapply function
parallel biocparallel
6.7 years ago felix.ernst • 0
2
votes
5
replies
2.5k
views
Issue with BiocParallel
purecn biocparallel
5.5 years ago milos-91 • 0
2
votes
3
replies
2.7k
views
BiocParallel::bplapply() performance with MulticoreParam() is worse than mclapply()
biocparallel parallel
6.9 years ago davide risso ▴ 950
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
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
2
votes
4
replies
3.0k
views
defaults in BiocParallel
biocparallel
updated 6.6 years ago by ★ 2.4k • written 9.6 years ago by ★ 6.5k
2
votes
2
replies
726
views
Number of MPI slaves in BiocParallel
BiocParallel
updated 4.2 years ago by 25k • written 4.2 years ago by • 0
2
votes
1
reply
1.3k
views
Build error: could not find function "bplapply"
biocparallel build report
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 180
2
votes
9
replies
3.9k
views
Unable to calculate in parallel what can be calculated on a for loop
biocparallel foreach org.hs.eg.db gostats
updated 7.4 years ago by 25k • written 7.5 years ago by ▴ 730
2
votes
3
replies
3.7k
views
BiocParallel example does not work any more (sbatch produced exit code 1)
biocparallel slurm
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by • 0
2
votes
2
replies
906
views
how to use biocParallel for large local variables?
BiocParallel
3.3 years ago oyoung122 ▴ 20
2
votes
2
replies
1.2k
views
bplapply slow to decide number of cores
biocparallel
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 180
1
vote
1
reply
2.2k
views
Error in summarizeOverlaps: Error in names(res) <- nms; 'names' attribute [15] must be the same length as the vector [2]
software error summarizeoverlaps biocParallel
7.6 years ago chriad ▴ 10
1
vote
10
replies
1.8k
views
bplapply 1.2.9 (and higher) breaks on Windows x64
biocparallel
8.8 years ago Lorenz • 0
1
vote
16
replies
2.3k
views
BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers on localhost
biocparallel
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 20
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 25k • written 4.8 years ago by ▴ 110
1
vote
2
replies
1.7k
views
BiocParallel and CopywriteR Error
bioconductor biocparallel copywriter
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 10
1
vote
4
replies
1.7k
views
TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writing to connection
TarSeqQC R ngs biocparallel
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 10
1
vote
4
replies
1.3k
views
BiocParallel 1.4.3: Error following example 4.2.1 - "Error in 0.4 * nx/tasks : non-numeric argument to binary operator"
biocparallel
8.1 years ago lee.tibbert ▴ 20
50 results • Page 1 of 1
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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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