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 6.0 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 3.9 years ago by 25k • written 3.9 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
8.9 years ago Sean Davis 21k
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 ★ 6.5k • written 5.6 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
2.9k
views
BiocParallel: database disk image is malformed
biocparallel databases
updated 5.9 years ago by 25k • written 5.9 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
925
views
bpaggregate with formula returns strange error message
biocparallel bpaggregate aggregate
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 180
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 16 months ago by ★ 5.2k • written 22 months ago by • 0
4
votes
3
replies
1.9k
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 6.9 years ago by ▴ 40 • written 7.0 years ago by • 0
4
votes
5
replies
1.3k
views
parRapply in BiocParallel ?
biocparallel variantannotation
updated 8.0 years ago by ★ 11k • written 8.0 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
834
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 7.8 years ago by 25k • written 7.8 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
208
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
24 days ago • updated 18 days ago jacques.imbert • 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 • 0 • written 3.5 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 ▴ 260
3
votes
3
replies
1.1k
views
Parallel reading of Vcfs using VcfStack/RangedVcfStack
GenomicFiles BiocParallel
updated 6.9 years ago by 3.9k • written 7.0 years ago by ▴ 20
3
votes
2
replies
1.0k
views
Getting data/objects to workers in bplapply inside a function
biocparallel
updated 6.6 years ago by 25k • written 6.6 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 5.2 years ago by ▴ 10
2
votes
1
reply
1.9k
views
Rsubread installation problem
Rsubread BiocParallel
updated 5.0 years ago by 50k • written 5.0 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
1.1k
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
737
views
Number of MPI slaves in BiocParallel
BiocParallel
updated 4.3 years ago by 25k • written 4.3 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
4.0k
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
3.8k
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
915
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 6.6 years ago by 25k • written 6.6 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
7.7 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
8.2 years ago lee.tibbert ▴ 20
50 results • Page 1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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