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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
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
1
vote
7
replies
1.3k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by
James W. MacDonald
66k • written 11 months ago by
kyliecode
• 0
1
vote
7
replies
1.7k
views
enrichGOgradient color change
clusterProfiler
updated 9 weeks ago by
Guido Hooiveld
★ 4.0k • written 6 months ago by
inna.gur
• 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
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
3
votes
7
replies
910
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
9 months ago
casco
▴ 10
0
votes
7
replies
508
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
sharangiiv
• 0
1
vote
7
replies
897
views
Permutation test in DESeq2?
DESeq2
updated 8 months ago by
Michael Love
42k • written 8 months ago by
michellewei
• 0
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
66k • written 6 months ago by
client.kashi
• 0
1
vote
7
replies
4.6k
views
Problems Installing biomaRt
biomaRt
updated 6 months ago by
James W. MacDonald
66k • written 2.1 years ago by
ksci
▴ 20
2
votes
7
replies
975
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
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
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 12 months ago by
Gordon Smyth
50k • written 12 months ago by
mohammedtoufiq91
▴ 10
6
votes
7
replies
800
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
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by
Gordon Smyth
50k • written 12.1 years ago by
Kripa R
▴ 180
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 23 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
3
votes
7
replies
5.5k
views
error with champ.load
champ
written 6.6 years ago by
o.giannakopoulou
▴ 10
0
votes
7
replies
452
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
7 weeks ago
needNGS
• 0
0
votes
7
replies
377
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
5 weeks ago • updated 29 days ago
hortense96
• 0
1
vote
7
replies
889
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
694
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 11 weeks ago by
danalvoronov
▴ 10 • written 5 months ago by
jfmay
• 0
2
votes
7
replies
1.9k
views
Issue with GSVA using dgCMatrix
GSVA
updated 11 weeks ago by
Moritz
▴ 10 • written 2.9 years ago by
resa
• 0
4
votes
7
replies
742
views
DESeq2 unable to handle large count values
DESeq2
updated 9 weeks ago by
Michael Love
42k • written 6 months ago by
robennet
• 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
66k • written 6 months ago by
BioES
• 0
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by
Gordon Smyth
50k • written 8.0 years ago by
nathan
• 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 10 months ago by
alexandresegers
▴ 20 • written 19 months ago by
jeremymsimon
▴ 20
1
vote
7
replies
1.9k
views
Error using champ.import
ChAMP
EPICv2
updated 5 weeks ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
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
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
2
votes
7
replies
440
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
14 days ago • updated 11 days ago
sajadahmad41454
• 0
5
votes
7
replies
498
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Amit
• 0
4
votes
7
replies
911
views
weird volcano plot
DESeq2
updated 11 weeks ago by
Shuning
• 0 • written 6 months ago by
shouzheng
▴ 10
2
votes
7
replies
652
views
How do you post on this forum?
pcaMethods
3 months ago
yousavdj
• 0
1
vote
7
replies
375
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
27 days ago • updated 26 days ago
pl23
• 0
0
votes
7
replies
1.2k
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
544
views
distanceToNearest
rtracklayer
ranges
distanceToNearest
4 months ago
robjohn70000
• 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
1
vote
7
replies
6.9k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 11 weeks ago by
Hervé Pagès
16k • written 6 months ago by
inzirio
▴ 10
0
votes
7
replies
705
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
1.1k
views
Fishpond/Swish Interaction Test Error
fishpond
swish
11 months ago
Miguel
▴ 20
0
votes
7
replies
470
views
DESeq2 filtering vs edgeR filtering
DESeq2
10 weeks ago • updated 8 weeks ago
fr8712ca-s
• 0
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
3
votes
7
replies
890
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 8 months ago by
Chris
▴ 10
6
votes
7
replies
982
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 7 months ago by
ATpoint
★ 4.1k • written 7 months ago by
jonas.freimuth
▴ 20
3
votes
7
replies
1.9k
views
Installing densvis on a Singularity container
densvis
docker
updated 11 months ago by
alan.ocallaghan
▴ 160 • written 13 months ago by
James W. MacDonald
66k
0
votes
7
replies
761
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 29 days ago
shepherl
3.9k
0
votes
7
replies
1.9k
views
error with champ.load
ChAMP
champ
methylation
updated 9 months ago by
mike
• 0 • written 4.1 years ago by
jkong
• 0
8
votes
6
replies
513
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Amit
• 0
1,748 results • Page
4 of 35
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Comment: pathview error
by
Guido Hooiveld
★ 4.0k
> Will removing the NA values help solve the problem? Did you try? And, FWIW, in the cases I had ensembl-based RNA-seq datasets removed a…
Comment: pathview error
by
Fara
• 0
Thank you for the reply. I already conducted the KEGG enrichment analysis and I got the pathway ID. So there is no doubt it cannot be map…
Comment: Not able to install any Bioconductor 3.18 package [unable to access index]
by
bravaccinimirea
• 0
I am experiencing the same problem, I tried with all the advices I found in similar posts but nothing seems to work
Comment: can't open mghp.osn.xsede.org
by
merv
▴ 120
Seeing this issue today, now with the R 4.3 + Bioc 3.18 version of this package. It is the Bioconductor servers that redirect to this unrel…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf
by
Brandon
▴ 20
I did try again...*repeatedly*...I even tried it on a VM. Thankfully I got it to work on the VM. I still can't get it to work on windows t…
Votes
can't open mghp.osn.xsede.org
Answer: can't open mghp.osn.xsede.org
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Comment: recount3 problem downloading data from source sra
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