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2
replies
227
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
4 days ago • updated 1 day ago
BioinfGuru
▴ 30
0
votes
2
replies
102
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
1 day ago
makala
• 0
0
votes
2
replies
818
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
2
replies
929
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by
araaaju
• 0
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
28 days ago • updated 26 days ago
catv
• 0
0
votes
2
replies
948
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 3 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
1
vote
2
replies
400
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
Kim
• 0
1
vote
2
replies
740
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 22 days ago
Patadù
▴ 10
0
votes
2
replies
190
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 25 days ago by
taur.vil
• 0
1
vote
2
replies
369
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 14 days ago
Kim
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 17 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
2
votes
2
replies
224
views
fgsea significant result
fgsea
13 days ago • updated 12 days ago
Chris
▴ 10
0
votes
2
replies
93
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
5 days ago • updated 3 days ago
Yveto
• 0
2
votes
2
replies
271
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
10 days ago • updated 5 days ago
zzrammal
• 0
0
votes
2
replies
281
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 28 days ago
isaac.vock
• 0
2
votes
2
replies
234
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
18 days ago
Chris
▴ 10
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 8 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
2
replies
226
views
PCA plot suggestions
DESeq2
PCAtools
updated 21 days ago by
Michael Love
42k • written 23 days ago by
Aaliya
• 0
0
votes
2
replies
147
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
29 days ago
prity6459
• 0
0
votes
2
replies
161
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Espresso
• 0
0
votes
2
replies
749
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 2 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
2
replies
60
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 50 minutes ago by
Michael Love
42k • written 22 hours ago by
shaunpeterson
• 0
1
vote
2
replies
259
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
9 days ago • updated 8 days ago
Dylan.Sheerin
• 0
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 12 days ago by
Michael Love
42k • written 12 days ago by
mat149
▴ 70
0
votes
1
reply
173
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
z_bahari
• 0
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by
Michael Love
42k • written 24 days ago by
i.sudbery
▴ 40
2
votes
1
reply
67
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 3 days ago by
Alejandro Reyes
★ 1.9k • written 4 days ago by
Sara
• 0
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
1
vote
1
reply
153
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 21 days ago by
Leo Lahti
▴ 40 • written 22 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
262
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
SSSJec
• 0
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 26 days ago by
James W. MacDonald
65k • written 28 days ago by
John
• 0
3
votes
1
reply
147
views
How to save the DEXSeq results
DEXSeq
updated 12 days ago by
Michael Love
42k • written 12 days ago by
Sara
• 0
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 10 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
0
votes
1
reply
125
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 23 days ago by
Michael Love
42k • written 23 days ago by
kcarey
• 0
0
votes
1
reply
126
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 5 days ago by
Guido Hooiveld
★ 4.0k • written 5 days ago by
aogunbaw
• 0
1
vote
1
reply
156
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
marcusn
• 0
0
votes
1
reply
135
views
putting my own expression data in deseq2
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Dev
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
1
reply
86
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 3 days ago by
Michael Love
42k • written 4 days ago by
piemmea
• 0
2
votes
1
reply
167
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
e1271094
• 0
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 9 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
0
votes
1
reply
107
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 11 days ago by
shepherl
3.9k • written 11 days ago by
cyril.dalmasso
• 0
0
votes
1
reply
170
views
ATACseq merge peaks
DiffBind
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Shloka
• 0
0
votes
1
reply
132
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 16 days ago by
4r-rtg
• 0
0
votes
1
reply
166
views
Adding columns to DEXSeqResults object
DEXSeq
updated 29 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
0
votes
1
reply
158
views
rlog transformation
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
fernanda.backsouza
▴ 10
1
vote
1
reply
185
views
Handling multiple differential expression comparisons
DESeq2
updated 13 days ago by
Michael Love
42k • written 14 days ago by
Zainab
▴ 10
0
votes
1
reply
100
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 9 days ago by
ATpoint
★ 4.1k • written 9 days ago by
sajadahmad41454
• 0
186 results • Page
3 of 4
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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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