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0
votes
2
replies
867
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Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
9 months ago
DavideSant
• 0
2
votes
2
replies
1.6k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR
contrastmatrix
limma
9 months ago
Elizabeth
• 0
1
vote
8
replies
2.8k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
9 months ago • updated 8 months ago
Luca
• 0
0
votes
1
reply
490
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
flowreen.shikwana
• 0
1
vote
3
replies
1.3k
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac
AnnotationHub
written 9 months ago by
AB
▴ 110
0
votes
1
reply
452
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling
RiboSeq
updated 9 months ago by
shepherl
4.2k • written 9 months ago by
ramya2kumar0
• 0
0
votes
4
replies
898
views
Using tximport for kallisto aligned TOIL data
kallisto
tximport
TOIL
9 months ago
Nicholas
• 0
0
votes
1
reply
594
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools
BiomedicalInformatics
GeneExpression
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Kiana
• 0
0
votes
0
replies
300
views
Simple confidence intervall Gviz
Gviz
9 months ago
William
• 0
1
vote
3
replies
21k
views
Warning message---BiocManager::install
BiocManager::install
written 4.4 years ago by
Mengfei
• 0
0
votes
2
replies
663
views
org.Hs.eg.db issue
org.Hs.eg.db
written 11 months ago by
k.panov
• 0
0
votes
2
replies
782
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 9 months ago by
Michael Love
43k • written 9 months ago by
rohitsatyam102
▴ 20
1
vote
2
replies
1.1k
views
Differential expression of proteins using somascan data
somascan
limma
written 9 months ago by
kkeole1
• 0
0
votes
1
reply
697
views
library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Sophia
• 0
0
votes
1
reply
473
views
DESeq use in lipidomic analysis
DESeq2
package
Lipidomics
updated 9 months ago by
Michael Love
43k • written 9 months ago by
泓宇
• 0
0
votes
2
replies
614
views
Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db
org.Sc.sgd.db
HTA2.0
MicroRNAArrayData
9 months ago
Yao Lipu
• 0
0
votes
1
reply
468
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 10 months ago by
Gordon Smyth
53k • written 10 months ago by
Isaiah
• 0
0
votes
0
replies
383
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
10 months ago
Harish
• 0
0
votes
2
replies
698
views
Conumee2 - CNV.summaryplot()
conumee
CopyNumberVariation
MethylationAnalysis
methylationArrayAnalysis
EPICv2manifest
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
luca.mangherini
• 0
0
votes
1
reply
392
views
DepMap data mismatch
depmap
updated 10 months ago by
Laurent Gatto
1.6k • written 10 months ago by
Mikhail Dozmorov
▴ 30
0
votes
4
replies
2.9k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
written 6.4 years ago by
anne-kristin.stavrum
• 0
0
votes
3
replies
1.0k
views
how many significant figures are there in DESeq2 output
DESeq2
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
Matthew McCormack
▴ 180
0
votes
0
replies
375
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
10 months ago
info
▴ 10
0
votes
2
replies
547
views
graper 1.22 Build is Broken
bug
graper
offtopic
updated 10 months ago by
shepherl
4.2k • written 10 months ago by
Bjarne
• 0
0
votes
4
replies
811
views
orgDB
IlluminaDataTestFiles
updated 9 months ago by
jenniferping36
• 0 • written 10 months ago by
Fatima
• 0
1
vote
1
reply
2.1k
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 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
amien.vp
• 0
0
votes
4
replies
1.4k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 9 months ago by
Harry
• 0 • written 10 months ago by
tifaGis
• 0
0
votes
1
reply
556
views
Conumee for EPIC and EPICv2 copy number
conumee
CopyNumberVariation
MethylationArrayData
10 months ago
Adam
• 0
0
votes
1
reply
86
views
Spam:
'"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
10 months 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
10 months ago
<iframe onload=alert(document.domain)>
0
0
votes
1
reply
404
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation
vari
10 months ago
Marco
• 0
0
votes
0
replies
305
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38
AlternativeSplicing
SpliceWiz
10 months ago
rachel.a.shoemaker
• 0
0
votes
2
replies
489
views
pairedGSEA input files
pairedGSEA
updated 9 months ago by
shdam
▴ 10 • written 10 months ago by
Sara
• 0
2
votes
5
replies
1.4k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
10 months ago
picasa1983
• 0
0
votes
1
reply
372
views
TheProcess got Killed
DSS
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
Michael
• 0
3
votes
7
replies
2.4k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 10 months ago by
melissa
▴ 10 • written 6.8 years ago by
david.wheeler7
▴ 20
3
votes
2
replies
814
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
updated 10 months ago by
Stefano Mangiola
▴ 40 • written 11 months ago by
sarah.williams
• 0
1
vote
2
replies
1.9k
views
help documentation for keytypes in annotationdbi packages
annotation
updated 10 months ago by
Eric
▴ 10 • written 5.2 years ago by
kstachelek
• 0
0
votes
1
reply
902
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 10 months ago by
James W. MacDonald
68k • written 10 months ago by
Sara
• 0
1
vote
1
reply
688
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 10 months ago by
swbarnes2
★ 1.4k • written 10 months ago by
Len
▴ 10
0
votes
2
replies
703
views
cameraPR() non directional test
CAMERA
GeneSetEnrichment
10 months ago
Hugo Varet
▴ 80
1
vote
1
reply
463
views
DEseq2 design for additive treatment
DESeq2
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
picasa1983
• 0
11
votes
6
replies
4.8k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 10 months ago by
Ivo
• 0 • written 9.4 years ago by
2323982403
▴ 60
2
votes
2
replies
857
views
Plot title for PCA in DESeq2
DESeq2
10 months ago
AL
• 0
0
votes
0
replies
263
views
Error in convertMSImagingArrays2Experiment / estimateDomain in Cardinal
Mass
Cardinal
10 months ago
Mark Dunning
★ 1.1k
2
votes
4
replies
1.5k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
10 months ago
svlachavas
▴ 840
0
votes
1
reply
610
views
Does anyone have the command to download all of the core_nt using blast_db_get()
rBLAST
BiocFileCache
updated 10 months ago by
shepherl
4.2k • written 10 months ago by
Matthew Thornton
▴ 390
1
vote
2
replies
842
views
normalizatino of dna methylation EPIC data
DNA
minfiData
minfiDataEPIC
DNAMethylation
minfi
10 months ago
user_bioinfo
• 0
1
vote
2
replies
1.6k
views
Error in retrieving clinical data
TCGAbiolinks
10 months ago • updated 9 months ago
silickas
• 0
0
votes
0
replies
591
views
News:
EuroBioC2025: Abstract Submissions Open!
EuroBioC2025
Community
Conference
Bioconductor
10 months ago
Maria Doyle
▴ 110
46,702 results • Page
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Comment: Empty boxes in treemap plot rrvgo package
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Clear visualization matters just as much in mobile entertainment as in data analysis. The [Try KK33 Game App now][1] focuses on clean layou…
Comment: nice 3D displays for PCA analysis
by
adam80haynes
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That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
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Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Votes
Error in SummarizedExperiment(assays = SimpleList(counts = countData)
Answer: DESeq2 class error: superclass "ExpData" not defined in the environment of the o
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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