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Parallel
•
reset
0
votes
0
replies
600
views
set.seed in function vs clusterSetRNGStream: switching from one to another
parallel
seed
22 months ago
ZheFrench
▴ 40
0
votes
1
reply
946
views
Running limma in parallel
parallel
R
limma
EWAS
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
Lorenzo
• 0
3
votes
4
replies
1.4k
views
DiffBind (Error in if (DBA$config$parallelPackage))
parallel
R
DiffBind
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.7 years ago by
eggrandio
• 0
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
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
1
reply
530
views
Using multiple cores SCTensor package
SCTensor
Single Cell RNA Seq
Parallel
4.4 years ago
ieuangw
• 0
0
votes
4
replies
1.6k
views
DESeq2 using many cores despite parallel = FALSE
deseq2
parallel
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
symbiologist
• 0
6
votes
12
replies
1.8k
views
mclapply to loop over a GRangesList object
GenomicRanges
GRanges
GRangesList
parallel
mclapply
5.2 years ago
foehn
▴ 100
0
votes
0
replies
1.2k
views
miR2Pathway Finite Observations
pathway analysis
mirna
parallel
6.1 years ago
genomic8328
▴ 10
0
votes
1
reply
974
views
DiffBind count warning
diffbind
parallel
updated 6.2 years ago by
Rory Stark
★ 5.2k • written 6.2 years ago by
ghosos
• 0
1
vote
5
replies
2.4k
views
DiffBind does not run in parallel
diffbind
parallel
biocparallel
updated 6.3 years ago by
Rory Stark
★ 5.2k • written 6.3 years ago by
eggrandio
• 0
3
votes
3
replies
1.6k
views
BiocParallel: zombie processes on FORK cluster
biocparallel
parallel
updated 6.3 years ago by
Martin Morgan
25k • written 6.3 years ago by
alserg
▴ 240
1
vote
0
replies
1.4k
views
Problems running oligo functions in parallel on a linux computer
biocparallel
oligo
rma
linux
parallel
6.3 years ago
s.munster
▴ 40
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
3
replies
2.7k
views
BiocParallel::bplapply() performance with MulticoreParam() is worse than mclapply()
biocparallel
parallel
6.9 years ago
davide risso
▴ 950
1
vote
1
reply
1.5k
views
sva: Parallel execution of sva()-function fails.
sva
parallel
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
maltethodberg
▴ 170
4
votes
1
reply
1.3k
views
Parallel Join Excessively Slow
biocparallel
curatedmetagenomicdata
parallel
dplyr
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
Lucas Schiffer
▴ 240
1
vote
6
replies
1.6k
views
Multithreading problems with qalign
quasr
parallel
updated 7.4 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 7.4 years ago by
kirt.onthank
• 0
0
votes
1
reply
1.2k
views
BiocParallel and variable scope in child processes
parallel
variable scope
fork
BiocParallel
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
dan.gatti
• 0
0
votes
1
reply
1.2k
views
error when genomeFile too big when running Quasr on >3 clusters
quasr
parallel
cluster
8.2 years ago
rna seq
▴ 90
0
votes
9
replies
2.2k
views
problem using >3 clusters with Quasr
quasr
parallel
updated 8.2 years ago by
Martin Morgan
25k • written 8.2 years ago by
rna seq
▴ 90
2
votes
4
replies
1.3k
views
Running HTSFilter in paralell
htsfilter
parallel
updated 8.3 years ago by
andrea.rau
▴ 80 • written 8.3 years ago by
Richard Yanicky
▴ 10
0
votes
4
replies
1.4k
views
Using iterators and foreach with doMC, using DNAStringSets
dnastringset
parallel
iterators
8.4 years ago
ben.ward
▴ 30
0
votes
3
replies
1.7k
views
DEXSeqHTML parallelization error
Parallel
DEXSeq
DEXSeqHTML
8.4 years ago
Neel Aluru
▴ 460
0
votes
1
reply
1.1k
views
Paralelization of maSigPro
maSigPro
parallel
8.6 years ago
gmdc
• 0
0
votes
1
reply
1.3k
views
News:
Course Announcement: Use R / Bioconductor for Sequence Analysis (Intermediate Course)
Course
RNA-Seq
Chip-seq
Parallel
News
9.1 years ago
Martin Morgan
25k
1
vote
1
reply
1.0k
views
trigger package fails at parallalization - Transcriptional Regulatory Inference from Genetics of ExpRession
trigger
parallel
processing
multicore
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
affennacken
• 0
27 results • Page
1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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