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2
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771
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Pairwise analysis of DESeq result and limma result
DESeq2
limma
2.0 years ago • updated 24 months ago
Lily Cheang
▴ 10
0
votes
4
replies
961
views
DESeq2 nomalize value
DESeq2
2.0 years ago • updated 24 months ago
史哲
• 0
0
votes
4
replies
2.0k
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 2.1 years ago by
Igor
• 0
0
votes
0
replies
636
views
What is the significance of DMR in DMRcate
DMRcate
2.0 years ago
chuanjiao6
• 0
0
votes
1
reply
739
views
Limitation on single file size and package size when developing Bioc package
packagedevelopment
datalimit
Bioconductor
updated 2.0 years ago by
Hervé Pagès
16k • written 2.0 years ago by
Xin Wang
• 0
2
votes
1
reply
817
views
Continuous variable to identify responder genes using DESeq2
DESeq2
rnaseqGene
DifferentialExpression
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
Abhishek Singh
▴ 20
7
votes
28
replies
9.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 2.0 years ago by
Gordon Smyth
53k • written 10.9 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
0
replies
475
views
HiCDCPlus differential interaction error
HiCDCPlus
2.0 years ago
Irene
• 0
0
votes
3
replies
1.2k
views
LOG2FC DESEQ2
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
ilaria.montali
• 0
0
votes
4
replies
3.8k
views
ChAMP - obtaining beta values using EPICv2 annotation
ChAMP
EPICv2
updated 15 months ago by
icecreamlover
• 0 • written 2.1 years ago by
ChunkyJones
• 0
2
votes
4
replies
1.3k
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
2.0 years ago • updated 23 months ago
thomas.heigl.ibk
• 0
0
votes
4
replies
1.2k
views
DNABarcodes-Installation Issue
DNABarcodes
Install
2.0 years ago
nk130
• 0
0
votes
0
replies
726
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
2.0 years ago
Thalita
• 0
1
vote
4
replies
1.4k
views
goseq, warning and strange plot from nullp
goseq
2.0 years ago
boczniak767
▴ 740
1
vote
1
reply
1.0k
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 23 months ago by
Yang Liao
▴ 450 • written 2.0 years ago by
Joe Marturano
▴ 10
0
votes
1
reply
654
views
How to control RAN-seq samples from different libraries
metaMSdata
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
jianyang.liu
• 0
0
votes
4
replies
1.1k
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
2.0 years ago
candacenewcome
• 0
0
votes
1
reply
459
views
unequal number of treatmets to control
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
shawaimuhyees
• 0
0
votes
2
replies
1.1k
views
Batch effects removal across mRNA seq studies addressing different biological question: Best approach?
DESeq2
2.0 years ago
Kuldeep
• 0
0
votes
2
replies
892
views
PCA after DESeq2
DESeq2
PrincipalComponent
prin
DifferentialExpression
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
Shaimaa Gamal
• 0
1
vote
2
replies
1.1k
views
Longitudinal analysis in Limma
limma
2.0 years ago
COPD_Project
• 0
0
votes
0
replies
442
views
Postdoc
TCGAWorkflow
2.0 years ago
sameerahmadguru
• 0
0
votes
2
replies
983
views
DESeq2 lfcShrink drastic shrinkage
DESeq2
updated 10 months ago by
Nick
• 0 • written 2.0 years ago by
theophile
• 0
1
vote
1
reply
1.0k
views
Transcript level expression for CCLE
recount3
recount
CCLE
updated 2.0 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.0 years ago by
António Miguel de Jesus Domingues
▴ 510
6
votes
9
replies
4.4k
views
biomaRt has encountered an unknown server error.
biomaRt
host
useEnsembl
updated 2.0 years ago by
alexander3
• 0 • written 2.0 years ago by
Amparo
• 0
3
votes
3
replies
2.4k
views
plotUMAP Gene Set Faceted
scater
updated 2.0 years ago by
alan.ocallaghan
▴ 160 • written 2.0 years ago by
Dario Strbenac
★ 1.6k
0
votes
4
replies
1.6k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts
Rsubread
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
tjgray4
• 0
4
votes
6
replies
1.8k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
2.0 years ago
isaac.vock
• 0
2
votes
2
replies
1.3k
views
Using limma for controlling age variable
linearmodeling
limma
2.0 years ago
Matej
• 0
1
vote
3
replies
1.3k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
2.0 years ago
island
• 0
1
vote
1
reply
757
views
Question about correction of confounders for EWAS
dss
DSS
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
chuanjiao6
• 0
0
votes
2
replies
2.5k
views
GO enrichment analysis does not show any pathways in my case
GO
EnrichmentBrowser
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
prity6459
• 0
4
votes
4
replies
1.0k
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 2.0 years ago by
James W. MacDonald
68k • written 2.1 years ago by
Geo
• 0
0
votes
0
replies
1.3k
views
News:
Note about packages submitted for Bioconductor 3.19
Release
Submission
release
Bioconductor
2.0 years ago
shepherl
4.3k
0
votes
4
replies
1.5k
views
DESeq2 aborting after upgrade
DESeq2
2.0 years ago • updated 23 months ago
Aarti
• 0
2
votes
6
replies
5.9k
views
Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
2.0 years ago • updated 23 months ago
Tobias
• 0
3
votes
2
replies
864
views
Question about DMRcate
DMRcate
dmrcate
2.0 years ago
chuanjiao6
• 0
1
vote
1
reply
1.0k
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 2.0 years ago by
alan.ocallaghan
▴ 160 • written 2.0 years ago by
Dario Strbenac
★ 1.6k
0
votes
2
replies
920
views
Cross-species analysis using DESeq2 - size factor computation
dese
DESeq2
2.0 years ago
pl23
• 0
6
votes
7
replies
1.3k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
aa.machado001
• 0
0
votes
2
replies
886
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus
RNASeqData
2.0 years ago
Diana
• 0
0
votes
1
reply
720
views
Annotatr Duplicate Entries
annotatr
AnnotationHub
written 2.0 years ago by
hayleyw
• 0
0
votes
0
replies
493
views
IlluminaHumanMethylation27kanno.ilmn12.hg19 package is mapped to hg18 genome
IlluminaHumanMethylation27kanno.ilmn12.hg19
2.0 years ago
Basti
▴ 780
2
votes
2
replies
776
views
News:
"Edit" button not working
Bioconductor
Website
SupportSite
written 2.0 years ago by
shepherl
4.3k
0
votes
0
replies
459
views
iSEE Difference Panel Missing
iSEEu
2.0 years ago
Dario Strbenac
★ 1.6k
1
vote
3
replies
1.2k
views
Big differences between biological replicates makes DESeq2 result 0
chipseq
DifferentialMethylation
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
rebw25
• 0
1
vote
3
replies
1.4k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 2.0 years ago by
georgii.vdovin
• 0
4
votes
1
reply
2.0k
views
When should I correct for batch effects
BatchEffect
SingleCellExperiment
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
NeuroDaniel
▴ 20
0
votes
2
replies
2.1k
views
Regressing out covariates from expression matrix for PCA visualization - can I use coefficients calculated in DESeq2??
DESeq2
2.0 years ago
tombate94
• 0
1
vote
8
replies
1.7k
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
sat
• 0
46,741 results • Page
34 of 935
Recent ...
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Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Tikaaa2sahaaaq2c
• 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase
by
DamionLedner99
• 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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