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9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 5 months ago by
amin8w
▴ 10 • written 6.8 years ago by
sina.nassiri
▴ 130
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 29 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 4 months ago by
Shaimaa Gamal
• 0 • written 7.2 years ago by
myprogramming2016
• 0
5
votes
7
replies
483
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Amit
• 0
3
votes
7
replies
882
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 8 months ago by
Chris
▴ 10
4
votes
7
replies
896
views
weird volcano plot
DESeq2
updated 10 weeks ago by
Shuning
• 0 • written 6 months ago by
shouzheng
▴ 10
8
votes
7
replies
1.2k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 5 months ago by
Daniel E. Weeks
▴ 30
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2
RNASeq
updated 4 months ago by
Gordon Smyth
50k • written 14 months ago by
Ilya
• 0
1
vote
7
replies
6.8k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 10 weeks ago by
Hervé Pagès
16k • written 6 months ago by
inzirio
▴ 10
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 8 months ago by
lucap
• 0 • written 3.1 years ago by
Marianna
▴ 20
6
votes
7
replies
968
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 6 months ago by
ATpoint
★ 4.1k • written 7 months ago by
jonas.freimuth
▴ 20
0
votes
7
replies
1.7k
views
Unable to install RefPlus - R=4.3.1, BiocManager=3.18
Install
instal
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
client.kashi
• 0
0
votes
7
replies
742
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 23 days ago
shepherl
3.9k
4
votes
7
replies
1.1k
views
Fishpond/Swish Interaction Test Error
fishpond
swish
11 months ago
Miguel
▴ 20
6
votes
7
replies
599
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
aa.machado001
• 0
1
vote
7
replies
3.0k
views
Technical details of DiffBind correlation analysis
diffbind
duplicatecorrelation
updated 3 months ago by
Rory Stark
★ 5.2k • written 9.5 years ago by
meisan406
• 0
3
votes
7
replies
1.9k
views
Installing densvis on a Singularity container
densvis
docker
updated 11 months ago by
alan.ocallaghan
▴ 160 • written 12 months ago by
James W. MacDonald
65k
0
votes
7
replies
444
views
DESeq filtering specific to contrasts
DESeq2
updated 27 days ago by
Michael Love
42k • written 3 months ago by
Emma
• 0
1
vote
7
replies
874
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 5 months ago by
Gordon Smyth
50k • written 7 months ago by
Gimena
• 0
0
votes
7
replies
486
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
sharangiiv
• 0
2
votes
7
replies
4.8k
views
Installing Local packages in Bioconductor
package
updated 9 months ago by
Boxun
• 0 • written 2.0 years ago by
BioC123
• 0
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by
Gordon Smyth
50k • written 12.0 years ago by
Kripa R
▴ 180
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
1
vote
7
replies
4.5k
views
Problems Installing biomaRt
biomaRt
updated 6 months ago by
James W. MacDonald
65k • written 2.1 years ago by
ksci
▴ 20
6
votes
7
replies
793
views
Adding a group of samples reduces DEGs in other groups
RNASeq
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Jonathan
▴ 10
1
vote
7
replies
1.6k
views
enrichGOgradient color change
clusterProfiler
updated 8 weeks ago by
Guido Hooiveld
★ 4.0k • written 6 months ago by
inna.gur
• 0
0
votes
7
replies
353
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 24 days ago
hortense96
• 0
1
vote
7
replies
355
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
21 days ago • updated 20 days ago
pl23
• 0
2
votes
7
replies
537
views
distanceToNearest
rtracklayer
ranges
distanceToNearest
4 months ago
robjohn70000
• 0
0
votes
7
replies
1.8k
views
error with champ.load
ChAMP
champ
methylation
updated 9 months ago by
mike
• 0 • written 4.1 years ago by
jkong
• 0
0
votes
7
replies
1.7k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error
RStudio
ggplot2
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
BioES
• 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by
James W. MacDonald
65k • written 11 months ago by
kyliecode
• 0
2
votes
7
replies
356
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
9 days ago • updated 6 days ago
sajadahmad41454
• 0
1
vote
7
replies
889
views
Permutation test in DESeq2?
DESeq2
updated 8 months ago by
Michael Love
42k • written 8 months ago by
michellewei
• 0
2
votes
7
replies
1.8k
views
Issue with GSVA using dgCMatrix
GSVA
updated 10 weeks ago by
Moritz
▴ 10 • written 2.9 years ago by
resa
• 0
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
2
votes
7
replies
2.5k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 7 months ago by
dorota.komar
• 0 • written 3.4 years ago by
Ankit
▴ 20
0
votes
7
replies
1.4k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
13 months ago • updated 11 months ago
Ti
• 0
0
votes
7
replies
689
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 5 months ago by
Basti
▴ 780 • written 5 months ago by
486342583
• 0
4
votes
7
replies
731
views
DESeq2 unable to handle large count values
DESeq2
updated 8 weeks ago by
Michael Love
42k • written 6 months ago by
robennet
• 0
3
votes
7
replies
5.5k
views
error with champ.load
champ
written 6.5 years ago by
o.giannakopoulou
▴ 10
0
votes
7
replies
1.1k
views
Cannot open URL for StringDB protein.links.v11.5/9606.protein.links.v11.5.txt.gz
STRINGdb
updated 9 months ago by
damian.szk
▴ 80 • written 9 months ago by
Furkan
• 0
2
votes
7
replies
2.0k
views
How to generate custom annotation for rat genome rn6 in ChIPQC
ChIPQC
annotation
rn6
updated 4 months ago by
Raghavaram
• 0 • written 3.7 years ago by
Frédéric Crémazy
• 0
2
votes
7
replies
968
views
Errors with running learn.bn function and setting toCompact to TRUE in one.step.pigengene function in Pigengene package
Pigengene
6 months ago
kjngo
▴ 40
3
votes
7
replies
906
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
8 months ago
casco
▴ 10
0
votes
7
replies
434
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
6 weeks ago
needNGS
• 0
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2
rnaseq
statistics
updated 7 months ago by
camillab.
▴ 10 • written 6.6 years ago by
Russ Fraser
▴ 30
0
votes
7
replies
682
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 10 weeks ago by
danalvoronov
▴ 10 • written 5 months ago by
jfmay
• 0
2
votes
7
replies
638
views
How do you post on this forum?
pcaMethods
3 months ago
yousavdj
• 0
0
votes
7
replies
458
views
DESeq2 filtering vs edgeR filtering
DESeq2
9 weeks ago • updated 7 weeks ago
fr8712ca-s
• 0
1,738 results • Page
4 of 35
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Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning
by
angelaesper43
• 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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