Showing : biocparallel • reset
2
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5
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3.5k
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Issue with BiocParallel
purecn biocparallel
7.1 years ago milos-91 • 0
6
votes
8
replies
2.7k
views
BioParallel::BatchtoolsParam() - how to pass customized resource variables to batchtool's "slurm-simple" template using BatchtoolsParam()?
biocparallel BatchtoolsParam
updated 7.1 years ago by ★ 6.6k • written 7.1 years ago by ▴ 40
4
votes
2
replies
1.3k
views
bpaggregate with formula returns strange error message
biocparallel bpaggregate aggregate
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 180
5
votes
6
replies
3.6k
views
BiocParallel: database disk image is malformed
biocparallel databases
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 470
1
vote
1
reply
2.3k
views
Installing package BiocParallel failed
biocparallel
updated 7.5 years ago by 25k • written 7.5 years ago by ★ 1.3k
1
vote
5
replies
1.7k
views
Help using 'handler' function with bptry()
biocparallel error handling
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 760
12
votes
15
replies
4.9k
views
error with HDF5Array
hdf5array biocparallel
updated 7.6 years ago by ★ 6.6k • written 7.6 years ago by ▴ 30
0
votes
1
reply
1.8k
views
Write gds in parallel
gds SNPRelate BiocParallel
updated 7.6 years ago by ▴ 30 • written 7.6 years ago by ▴ 40
1
vote
6
replies
2.3k
views
Disable messages for bplapply when in parallel
biocparallel bplapply
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 30
0
votes
3
replies
2.5k
views
BiocParallel NULL value passed as symbol address
BiocParallel Rcpp
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 30
1
vote
2
replies
1.8k
views
bplapply with ShortRead functions
shortread biocparallel
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 100
1
vote
1
reply
1.8k
views
Error: BiocParallel errors; first error: invalid 'times' value
MBASED biocparallel
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 10
1
vote
5
replies
3.2k
views
DiffBind does not run in parallel
diffbind parallel biocparallel
updated 7.9 years ago by ★ 5.2k • written 7.9 years ago by • 0
2
votes
1
reply
1.7k
views
Build error: could not find function "bplapply"
biocparallel build report
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 180
3
votes
3
replies
2.1k
views
BiocParallel: zombie processes on FORK cluster
biocparallel parallel
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 280
1
vote
0
replies
1.9k
views
Problems running oligo functions in parallel on a linux computer
biocparallel oligo rma linux parallel
8.0 years ago s.munster ▴ 40
0
votes
4
replies
1.8k
views
DESeq2 Different Results when using different foreach parallel backends
deseq2 biocparallel
8.1 years ago • updated 8.0 years ago brnleehng • 0
2
votes
2
replies
1.7k
views
bplapply slow to decide number of cores
biocparallel
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 180
0
votes
0
replies
1.5k
views
Problem with BiocParallel::bpiterate
biocparallel bpiterate readGAlignmentPairs GenomicFiles::reduceByYield
8.2 years ago ioannis.vardaxis ▴ 30
3
votes
2
replies
1.5k
views
Getting data/objects to workers in bplapply inside a function
biocparallel
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 190
2
votes
4
replies
4.0k
views
defaults in BiocParallel
biocparallel
updated 8.2 years ago by ★ 2.4k • written 11.2 years ago by ★ 6.5k
2
votes
10
replies
2.9k
views
Correct way to load a package inside bplapply function
parallel biocparallel
8.3 years ago felix.ernst • 0
1
vote
2
replies
2.2k
views
BiocParallel and CopywriteR Error
bioconductor biocparallel copywriter
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 10
3
votes
3
replies
1.5k
views
Parallel reading of Vcfs using VcfStack/RangedVcfStack
GenomicFiles BiocParallel
updated 8.4 years ago by 4.2k • written 8.6 years ago by ▴ 20
4
votes
7
replies
6.9k
views
BiocParallel/scater warning after move to R 3.4.0
biocparallel scater
updated 8.4 years ago by ▴ 40 • written 8.6 years ago by • 0
1
vote
4
replies
2.2k
views
TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writing to connection
TarSeqQC R ngs biocparallel
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 10
5
votes
5
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2.0k
views
BiocParallel: messages shown only when processes finished
biocparallel
updated 8.5 years ago by 25k • written 8.5 years ago by ★ 2.1k
2
votes
3
replies
3.5k
views
BiocParallel::bplapply() performance with MulticoreParam() is worse than mclapply()
biocparallel parallel
8.5 years ago davide risso ▴ 980
0
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0
replies
876
views
Parallel version of viewApply?
viewApply biocparallel
8.6 years ago maltethodberg ▴ 180
0
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1
reply
1.5k
views
BiocParallel on Windows: how should I pass (not exported) setReplace functions to bplapply?
snowparam biocparallel
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 20
4
votes
5
replies
6.2k
views
BiocParallel on Windows : cannot find my functions when using SnowParam
BiocParallel SnowParam
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 60
4
votes
1
reply
1.8k
views
Parallel Join Excessively Slow
biocparallel curatedmetagenomicdata parallel dplyr
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 240
0
votes
8
replies
2.4k
views
`bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
biocparallel bplapply Suse error process
updated 9.0 years ago by • 0 • written 9.0 years ago by • 0
2
votes
9
replies
4.8k
views
Unable to calculate in parallel what can be calculated on a for loop
biocparallel foreach org.hs.eg.db gostats
updated 9.0 years ago by 25k • written 9.1 years ago by ▴ 760
5
votes
2
replies
1.8k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
9.4 years ago • updated 9.1 years ago Jurat Shahidin ▴ 80
0
votes
1
reply
1.6k
views
BiocParallel and variable scope in child processes
parallel variable scope fork BiocParallel
updated 9.1 years ago by 25k • written 9.1 years ago by • 0
0
votes
1
reply
1.5k
views
Question about sumbition process and biocviews
biocviews biocparallel github package submission
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 30
0
votes
3
replies
2.3k
views
BiocParallel exporting function?
biocparallel
9.1 years ago ioannis.vardaxis ▴ 30
4
votes
3
replies
2.9k
views
BiocParallel: object export issue
BiocParallel DOSE
updated 9.1 years ago by 25k • written 9.1 years ago by ★ 4.1k
2
votes
7
replies
3.2k
views
DESeq(): Forking of R Process even though parallel=FALSE
DESeq2 biocparallel
updated 9.2 years ago by 43k • written 9.2 years ago by • 0
1
vote
1
reply
2.5k
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
9.3 years ago chriad ▴ 10
0
votes
1
reply
1.4k
views
cant download biocparallel
biocparallel
updated 9.3 years ago by 25k • written 9.3 years ago by • 0
3
votes
4
replies
1.6k
views
bplapply stalling upon error with large data objects
biocparallel bplapply multicore
updated 9.3 years ago by 25k • written 9.4 years ago by ★ 29k
4
votes
5
replies
1.8k
views
parRapply in BiocParallel ?
biocparallel variantannotation
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 350
1
vote
16
replies
3.1k
views
BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers on localhost
biocparallel
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 20
1
vote
4
replies
1.7k
views
BiocParallel 1.4.3: Error following example 4.2.1 - "Error in 0.4 * nx/tasks : non-numeric argument to binary operator"
biocparallel
9.8 years ago lee.tibbert ▴ 20
3
votes
1
reply
1.1k
views
passing submitJobs parameters from BatchJobsParam
biocparallel
updated 9.8 years ago by 25k • written 9.8 years ago by ★ 1.9k
1
vote
2
replies
1.6k
views
Can bplapply timeout when waiting for long jobs?
biocparallel
updated 9.8 years ago by 25k • written 9.8 years ago by • 0
4
votes
4
replies
2.0k
views
Load balancing using BiocParallel
biocparallel
9.9 years ago t.kuilman ▴ 170
1
vote
2
replies
2.1k
views
BiocParallel::bplapply() performance issue
BiocParallel
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 30
115 results • Page 2 of 3
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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