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1
vote
2
replies
826
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GSVA 1.52.2 (new API) nb of workers?
parallelize
workers
GSVA
written 11 months ago by
johanna.galvis
• 0
0
votes
2
replies
291
views
How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignments?
GenomicAlignments
updated 1 day ago by
Hervé Pagès
16k • written 2 days ago by
Charles
• 0
4
votes
2
replies
407
views
GAlignments Cigar to GRanges
GenomicRanges
cigarRangesAlongReferenceSpace
GenomicAlignments
Cigar
1 day ago • updated 20 hours ago
pineiroalejandro
▴ 10
2
votes
3
replies
220
views
AnnotationHub/ExperimentHub resources backup
AnnotationHub
HubPub
ExperimentHub
updated 1 day ago by
James W. MacDonald
68k • written 1 day ago by
igor
▴ 50
6
votes
8
replies
5.0k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 5.1 years ago by
Colari19
▴ 60
0
votes
8
replies
3.8k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 2.1 years ago by
mauricio.microbiol
• 0
0
votes
0
replies
50
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
2 days ago
dudutchy
• 0
3
votes
1
reply
313
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2
apeglm
updated 2 days ago by
James W. MacDonald
68k • written 3 days ago by
sk
• 0
0
votes
0
replies
37
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
2 days ago
Muhammad
• 0
0
votes
0
replies
9
views
Spam:
County Group Wave City Ghaziabad
ri16cod.db
ncdfFlow
2 days ago
countywavecityghaziabad
0
1
vote
5
replies
957
views
Heatmap of a transformed deseq object with pheatmap
DESeq2
heatmaps
updated 2 days ago by
James W. MacDonald
68k • written 3 days ago by
caroline.zanchi
▴ 10
0
votes
0
replies
46
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
3 days ago
s.malik
• 0
0
votes
1
reply
193
views
Error in readCodelinkSet function
error
codelink
updated 3 days ago by
James W. MacDonald
68k • written 3 days ago by
nazaninhoseinkhan
• 0
0
votes
0
replies
75
views
Combat-seq usage
sva
updated 3 days ago by
ATpoint
★ 4.8k • written 4 days ago by
bbao
▴ 10
0
votes
1
reply
184
views
Best tximport quant.genes.sf
tximport
tximeta
Bioconductor
updated 3 days ago by
ATpoint
★ 4.8k • written 4 days ago by
yob4003
• 0
0
votes
1
reply
158
views
What happened to the Joost2016 dataset
org.Sc.sgd.db
updated 3 days ago by
shepherl
4.1k • written 6 days ago by
clementleong
• 0
2
votes
5
replies
859
views
Dealing with heteroscedascity in limma
limma
splines
Proteomics
written 9 days ago by
Thomas
• 0
0
votes
3
replies
50k
views
SingleR Label.Ont
SingleR
written 20 months ago by
saeed.khalili
• 0
0
votes
1
reply
345
views
News:
Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt
ensembldb
updated 6 days ago by
sophisticated.blackbird.meau
• 0 • written 8 days ago by
Aleena_Ensembl
▴ 30
5
votes
7
replies
2.8k
views
limma correction for tumor purity
limma
9 days ago • updated 3 days ago
gabriella.jacobson-eisenberg
▴ 20
0
votes
1
reply
242
views
Filtering out non-variable probes from EPICv2 matrix
DMRcate
EPICv2manifest
updated 9 days ago by
James W. MacDonald
68k • written 13 days ago by
Sasha
• 0
0
votes
1
reply
145
views
FlowSOM is unable to create Output
FlowSOM
updated 9 days ago by
ATpoint
★ 4.8k • written 9 days ago by
marco.klein1
• 0
8
votes
3
replies
2.4k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 7 days ago by
Michael Love
43k • written 10 days ago by
Cassia
▴ 40
2
votes
14
replies
2.6k
views
How to load scRNA-seq data from GEO
SingleCellExperiment
GEO
10 days ago • updated 5 days ago
petergrahamclark
• 0
0
votes
5
replies
487
views
Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
written 8 weeks ago by
Wolfgang RAFFELSBERGER
▴ 140
0
votes
4
replies
1.0k
views
compute_fasta_digest does not match Salmon index hash
tximeta
written 7 weeks ago by
Alex
• 0
1
vote
7
replies
3.3k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 10 days ago by
QFC
• 0 • written 2.1 years ago by
Oscar
▴ 10
2
votes
3
replies
1.3k
views
Filtering after DESeq
DESeq2
IHW
updated 10 days ago by
ChaseWendrix
• 0 • written 20 days ago by
caroline.zanchi
▴ 10
0
votes
4
replies
939
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
11 days ago • updated 5 days ago
sk
• 0
0
votes
3
replies
680
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR
limma
written 5 weeks ago by
skiaphrene
▴ 10
4
votes
6
replies
882
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
updated 1 hour ago by
Paul Harrison
▴ 110 • written 13 days ago by
caroline.zanchi
▴ 10
0
votes
2
replies
650
views
Version conflict when pushing to scQTLtools devel branch
Bioconductor
written 29 days ago by
XFWu
• 0
2
votes
5
replies
1.5k
views
Unable to install a forged BSgenome package
BSgenomeForge
updated 10 days ago by
James W. MacDonald
68k • written 14 days ago by
JABEZ RAJU
• 0
1
vote
2
replies
1.1k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
updated 14 days ago by
James W. MacDonald
68k • written 15 days ago by
Franz Bachmann
• 0
0
votes
3
replies
610
views
Discrepancies in normalised count data vs unnormalised
DESeq2
updated 10 days ago by
swbarnes2
★ 1.4k • written 15 days ago by
AMgroup
• 0
0
votes
2
replies
476
views
Design formula for circadian time-course data for vst() function
DESeq2
16 days ago
Vishnu
• 0
0
votes
5
replies
649
views
Check removeBatchEffect effectiveness
RNAseq
limma
removeBatchEffect
18 days ago • updated 18 hours ago
massimo
• 0
0
votes
0
replies
241
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
19 days ago
jamiecatalano2
• 0
1
vote
3
replies
1000
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 20 days ago by
James W. MacDonald
68k • written 22 days ago by
Carolina
• 0
0
votes
1
reply
262
views
RNA-seq input to GRaNIE
GRaNIE
updated 21 days ago by
James W. MacDonald
68k • written 21 days ago by
maia.malonzo
• 0
0
votes
1
reply
508
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub
GOSemSim
rrvgo
updated 21 days ago by
sergisayolspuig
▴ 80 • written 6 months ago by
daccar98
• 0
0
votes
2
replies
598
views
Analyzing TnSeq data with DESeq2
DESeq2
written 22 days ago by
newfunland
• 0
1
vote
5
replies
1.5k
views
Package developing and interoperation with Bioconductor
Package
Bioconductor
written 7 weeks ago by
slizchap
• 0
0
votes
2
replies
760
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
22 days ago • updated 19 hours ago
Kateřina
• 0
0
votes
6
replies
1.7k
views
News:
EuroBioC2024 abstract submission is open!
Conference
Bioconductor
EuroBioC2024
written 15 months ago by
Maria Doyle
▴ 100
2
votes
1
reply
450
views
ROAST for small sets
limma
mroast
updated 22 days ago by
Gordon Smyth
52k • written 23 days ago by
Jay
• 0
0
votes
1
reply
914
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2
RUVSeq
updated 23 days ago by
Michael Love
43k • written 7 weeks ago by
Simran
• 0
0
votes
2
replies
505
views
Differing results with DESeq2
DESeq2
updated 21 days ago by
JKim
• 0 • written 5 weeks ago by
hampsdiv
• 0
0
votes
1
reply
111
views
Make DEXSeq plot normal scale
DEXSeq
Dexseq
updated 23 days ago by
James W. MacDonald
68k • written 24 days ago by
Rico
• 0
0
votes
2
replies
372
views
RNA Seq using Lrt
DESeq2
23 days ago • updated 22 days ago
Rob
• 0
46,495 results • Page
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Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Geoff
• 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Comment: cannot download atena annotation for human
by
Davide
• 0
Hi Robert, I was able to solve the problem. Indeed, it stems from the co-occurrence of two different AnnotationHub available for hg38. …
Comment: Setting ylims in bam coverage plot and assigning compound sashimi numbers to ove
by
macdonaldfrench7286566
• 0
Regarding the ylim for the coverage [space waves][1], have you tried accessing the ylim slot of the CoverageTrack object after you've creat…
Votes
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
Answer: GAlignments Cigar to GRanges
parameters of filterByExpr
Answer: parameters of filterByExpr
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