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replies
16
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
15 hours ago
DavideSant
• 0
1
vote
1
reply
294
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR
contrastmatrix
limma
updated 1 day ago by
James W. MacDonald
68k • written 2 days ago by
Elizabeth
• 0
1
vote
2
replies
519
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
2 days ago • updated 1 day ago
Luca
• 0
0
votes
1
reply
211
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 1 day ago by
James W. MacDonald
68k • written 2 days ago by
flowreen.shikwana
• 0
1
vote
2
replies
446
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac
AnnotationHub
3 days ago • updated 2 days ago
AB
▴ 110
0
votes
1
reply
139
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling
RiboSeq
updated 2 days ago by
shepherl
4.1k • written 2 days ago by
ramya2kumar0
• 0
0
votes
3
replies
369
views
Using tximport for kallisto aligned TOIL data
kallisto
tximport
TOIL
updated 3 days ago by
James W. MacDonald
68k • written 7 days ago by
Nicholas
• 0
0
votes
1
reply
242
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools
BiomedicalInformatics
GeneExpression
updated 3 days ago by
James W. MacDonald
68k • written 4 days ago by
Kiana
• 0
0
votes
0
replies
32
views
Simple confidence intervall Gviz
Gviz
3 days ago
William
• 0
1
vote
3
replies
19k
views
Warning message---BiocManager::install
BiocManager::install
written 3.6 years ago by
Mengfei
• 0
0
votes
2
replies
331
views
org.Hs.eg.db issue
org.Hs.eg.db
written 8 weeks ago by
k.panov
• 0
0
votes
1
reply
173
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 4 days ago by
ATpoint
★ 4.7k • written 4 days ago by
rohitsatyam102
▴ 20
1
vote
2
replies
648
views
Differential expression of proteins using somascan data
somascan
limma
written 6 days ago by
kkeole1
• 0
4
votes
4
replies
841
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
8 days ago • updated 6 days ago
Elijah
• 0
0
votes
1
reply
202
views
library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 7 days ago by
James W. MacDonald
68k • written 7 days ago by
Sophia
• 0
0
votes
1
reply
154
views
DESeq use in lipidomic analysis
DESeq2
package
Lipidomics
updated 7 days ago by
Michael Love
43k • written 8 days ago by
泓宇
• 0
0
votes
7
replies
2.4k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 7 days ago by
robert
• 0 • written 23 months ago by
Oscar
• 0
0
votes
2
replies
295
views
Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db
org.Sc.sgd.db
HTA2.0
MicroRNAArrayData
7 days ago • updated 6 days ago
Yao Lipu
• 0
0
votes
1
reply
178
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 9 days ago by
Gordon Smyth
52k • written 9 days ago by
Isaiah
• 0
0
votes
0
replies
56
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
9 days ago
Harish
• 0
0
votes
1
reply
111
views
myvariant error
myvariant
getVariants
updated 9 days ago by
James W. MacDonald
68k • written 10 days ago by
Christelle
• 0
0
votes
2
replies
166
views
Conumee2 - CNV.summaryplot()
conumee
CopyNumberVariation
MethylationAnalysis
methylationArrayAnalysis
EPICv2manifest
updated 9 days ago by
James W. MacDonald
68k • written 9 days ago by
luca.mangherini
• 0
0
votes
1
reply
125
views
DepMap data mismatch
depmap
updated 9 days ago by
Laurent Gatto
1.6k • written 9 days ago by
Mikhail Dozmorov
▴ 30
0
votes
4
replies
2.3k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 5 days ago by
California Business Journal
• 0 • written 5.6 years ago by
anne-kristin.stavrum
• 0
0
votes
3
replies
583
views
how many significant figures are there in DESeq2 output
DESeq2
updated 11 days ago by
ATpoint
★ 4.7k • written 13 days ago by
Matthew McCormack
▴ 180
0
votes
0
replies
81
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
13 days ago
info
▴ 10
0
votes
2
replies
217
views
graper 1.22 Build is Broken
bug
graper
offtopic
updated 13 days ago by
shepherl
4.1k • written 13 days ago by
Bjarne
• 0
0
votes
1
reply
79
views
cannot download atena annotation for human
atena
13 days ago
Davide
• 0
0
votes
4
replies
362
views
orgDB
IlluminaDataTestFiles
updated 3 days ago by
jenniferping36
• 0 • written 13 days ago by
Fatima
• 0
1
vote
1
reply
542
views
GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct" and "unused arguments (exprsData = as.matrix(rna_seq_sub), gset.idx…
GSVA
updated 13 days ago by
ATpoint
★ 4.7k • written 13 days ago by
amien.vp
• 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 8 days ago by
Harry
• 0 • written 14 days ago by
tifaGis
• 0
0
votes
1
reply
175
views
Conumee for EPIC and EPICv2 copy number
conumee
CopyNumberVariation
MethylationArrayData
14 days ago • updated 13 days ago
Adam
• 0
0
votes
1
reply
85
views
Spam:
'"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
14 days ago
<iframe onload=alert(document.domain)>
0
0
votes
0
replies
17
views
Spam:
<iframe onload=alert(document.domain)>
ncdfFlow
MethylSeekR
cadd.v1.6.hg38
org.Sc.sgd.db
MafDb.1Kgenomes.phase1.GRCh38
14 days ago
<iframe onload=alert(document.domain)>
0
0
votes
1
reply
164
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation
vari
14 days ago • updated 13 days ago
Marco
• 0
0
votes
0
replies
39
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38
AlternativeSplicing
SpliceWiz
14 days ago
rachel.a.shoemaker
• 0
0
votes
1
reply
188
views
pairedGSEA input files
pairedGSEA
updated 14 days ago by
James W. MacDonald
68k • written 15 days ago by
Sara
• 0
2
votes
5
replies
966
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
15 days ago • updated 14 days ago
picasa1983
• 0
0
votes
1
reply
150
views
TheProcess got Killed
DSS
updated 14 days ago by
James W. MacDonald
68k • written 15 days ago by
Michael
• 0
3
votes
7
replies
2.0k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 14 days ago by
melissa
▴ 10 • written 6.0 years ago by
david.wheeler7
▴ 20
3
votes
2
replies
414
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
updated 15 days ago by
Stefano Mangiola
▴ 40 • written 8 weeks ago by
sarah.williams
• 0
1
vote
2
replies
1.5k
views
help documentation for keytypes in annotationdbi packages
annotation
updated 15 days ago by
Eric
▴ 10 • written 4.4 years ago by
kstachelek
• 0
0
votes
1
reply
303
views
How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData
DESeq2
pseudobulk
sing
updated 16 days ago by
James W. MacDonald
68k • written 16 days ago by
Sara
• 0
1
vote
1
reply
432
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 17 days ago by
swbarnes2
★ 1.4k • written 17 days ago by
Len
▴ 10
0
votes
2
replies
379
views
cameraPR() non directional test
CAMERA
GeneSetEnrichment
21 days ago • updated 17 days ago
Hugo Varet
▴ 80
1
vote
1
reply
271
views
DEseq2 design for additive treatment
DESeq2
updated 17 days ago by
ATpoint
★ 4.7k • written 18 days ago by
picasa1983
• 0
11
votes
6
replies
4.2k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 19 days ago by
Ivo
• 0 • written 8.6 years ago by
2323982403
▴ 60
2
votes
2
replies
487
views
Plot title for PCA in DESeq2
DESeq2
20 days ago • updated 16 days ago
AL
• 0
0
votes
0
replies
86
views
Error in convertMSImagingArrays2Experiment / estimateDomain in Cardinal
Mass
Cardinal
20 days ago
Mark Dunning
★ 1.1k
2
votes
4
replies
853
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
22 days ago • updated 9 days ago
svlachavas
▴ 840
46,392 results • Page
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Comment: Can't post a question?
by
DavideSant
• 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data
by
silickas
• 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
Comment: deseq2 lfc shrinkage with few DEGs
by
Robert
• 0
I'm dealing with a similar situation. I assume the coefficients related to batch effect would need to be included in idx also, is this corr…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
Thank you so much!! Yeah I had thought about this too, regarding the fact that DiffBind is a wrapper for counting peaks in this way in R di…
Comment: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
by
aitor
• 0
Hi everyone. I have a RIP-Seq analysis with 3 conditions and 3 assays (IP, IgG and Input for each of them). 4 replicates for each conditio…
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Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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