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0
votes
0
replies
11
views
Choosing between voomLmFit() and DREAM() when they identify very different sets of DEGs
limma
55 minutes ago
Emmanuel
• 0
0
votes
0
replies
21
views
Issue using barplot function in r
clusterProfiler
Bioconductor
enrichGO
barplot
6 hours ago
GA
▴ 10
0
votes
1
reply
61
views
Pathview not mapping all gene names in diagram
pathview
DESeq2
updated 10 hours ago by
Guido Hooiveld
★ 4.1k • written 1 day ago by
fonsvandehare
• 0
1
vote
1
reply
115
views
Diffbind using EdgeR
DiffBind
edgeR
updated 3 days ago by
Gordon Smyth
53k • written 6 days ago by
Nico
• 0
1
vote
4
replies
2.0k
views
Can't produce a generegiontrack from my txdb anymore
gviz
GenomicFeatures
written 4.7 years ago by
A.J.
▴ 20
3
votes
6
replies
482
views
DESeq2 single factor multiple levels, log of ratio or ratio of log ?
dese
scrna
scRNAseq
DESeq2
written 12 days ago by
Naomie
• 0
0
votes
0
replies
75
views
Differential miRNAome analysis for miRNA-generating protein mutant
Normalization
DESeq2
miRNA
DifferentialExpression
7 days ago
jpt8069
• 0
0
votes
3
replies
206
views
scRNA compositional analysis tools
scRNAseq
scCODA
propeller
scikit
updated 7 days ago by
ATpoint
★ 5.0k • written 8 days ago by
soumyaya21
• 0
0
votes
7
replies
2.4k
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
written 3.1 years ago by
Maria Doyle
▴ 110
0
votes
1
reply
126
views
Different GSEA results from same GEO dataset: Salmon vs TopHat pipeline
org.Mm.eg.db
tximport
DESeq2
clusterProfiler
updated 8 days ago by
ATpoint
★ 5.0k • written 9 days ago by
해연
• 0
0
votes
0
replies
8
views
Spam:
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Cepo
9 days ago
Akash
0
3
votes
1
reply
188
views
Blocking vs duplicateCorrelation for unbalanced designs in limma
limma
updated 13 days ago by
Gordon Smyth
53k • written 13 days ago by
A.Barden
▴ 20
0
votes
0
replies
18
views
Spam:
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BSgenome.Hsapiens.UCSC.hg17.masked
13 days ago
marinasky801
0
1
vote
2
replies
295
views
Permutation analysis/bootstrapping - DESeq2
DESeq2
updated 14 days ago by
James W. MacDonald
68k • written 14 days ago by
epocr
• 0
1
vote
3
replies
311
views
A question about limpa - multi level experiment
limpa
multi-level
updated 13 days ago by
Gordon Smyth
53k • written 16 days ago by
J Kim
▴ 10
0
votes
0
replies
79
views
Error in BMIQ initialization
BMIQ
wateRmelon
16 days ago
David
• 0
0
votes
1
reply
163
views
F-statistic cutoff for GSEA
clusterProfiler
GSEA
updated 20 days ago by
ATpoint
★ 5.0k • written 21 days ago by
siobhan.dietz
• 0
0
votes
0
replies
125
views
News:
Final call! BioC2026 abstract submissions are closing soon
Bioconductor
BioC2026
Conference
20 days ago
laurah ondari
• 0
1
vote
3
replies
223
views
Is psygenet2r still functional?
psygenet2r
Bioconductor
written 20 days ago by
Jon
• 0
1
vote
2
replies
271
views
How to remove/clean unwanted DEG data before downstream analysis?
DifferentialExpression
limma
updated 21 days ago by
James W. MacDonald
68k • written 21 days ago by
mishi
• 0
1
vote
3
replies
284
views
RNA-seq, point-by-point contrasts
edgeR
updated 16 days ago by
J Kim
▴ 10 • written 22 days ago by
boczniak767
▴ 750
2
votes
3
replies
360
views
Is it still possible to do batch correction for my data?
RNASeq
edgeR
27 days ago • updated 22 days ago
LBJ0744
• 0
0
votes
0
replies
194
views
News:
The BioC2026 Call for Abstracts deadline has been extended
Bioconductor
BioC2026
Conference
26 days ago
laurah ondari
• 0
0
votes
1
reply
244
views
specifying refColumn in calcNormFactors()
edgeR
limma
updated 26 days ago by
Gordon Smyth
53k • written 28 days ago by
Nova
• 0
0
votes
1
reply
279
views
Sex prediction in sesame for EPICV2
sesame
EPICv2manifest
updated 26 days ago by
Tim Peters
▴ 230 • written 27 days ago by
poojitha.stemcell
▴ 10
0
votes
0
replies
156
views
APAlyzer gives zero/NaN matrix?
APAlyzer
27 days ago
lynn.hua.lee
• 0
0
votes
4
replies
344
views
Convergence Issues and Model Selection DESeq2
DESeq2
28 days ago • updated 27 days ago
dani.guan.3
• 0
5
votes
3
replies
1.1k
views
Limma-voom sample weights and impact on DEG numbers
limma
written 3 months ago by
A.Barden
▴ 20
2
votes
2
replies
356
views
Quick two questions on limpa
limpa
updated 25 days ago by
Gordon Smyth
53k • written 29 days ago by
J Kim
▴ 10
0
votes
2
replies
237
views
recursively counting package dependencies
BiocPkgTools
4 weeks ago • updated 29 days ago
Helena
• 0
1
vote
2
replies
299
views
Subsetting DDS object for individual conditions over time
DESeq2
4 weeks ago
A
▴ 70
2
votes
2
replies
306
views
tximeta cannot open annotation gtf?
tximeta
Bioconductor
updated 5 weeks ago by
Michael Love
43k • written 5 weeks ago by
lynn.hua.lee
• 0
1
vote
2
replies
325
views
GSEA error
gsea
GSEABenchmarkeR
5 weeks ago • updated 4 weeks ago
Adithi
• 0
0
votes
0
replies
19
views
Spam:
TOGAF Certification Training in Dallas TX | Enterprise Architecture & ADM Mastery
mouse430a2.db
BSgenome.Hsapiens.UCSC.hg17.masked
5 weeks ago
zebaafarheensprintzeal
0
0
votes
3
replies
273
views
Unable to find ENTREZ IDs
entrezid
ensembldb
5 weeks ago
Adithi
• 0
0
votes
0
replies
14
views
Spam:
1. What is the CCIE Enterprise Infrastructure Certification?
TxDb.Dmelanogaster.UCSC.dm3.ensGene
DiseaseModel
5 weeks ago
Clarasmith
0
0
votes
1
reply
338
views
bcftools norm Equivalent
Rsamtools
written 10 weeks ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
464
views
Inconsistencies between accessor functions for TxDb databases with selected seqlevels.
TxDb
GenomicFeatures
GenomeInfoDb
written 7 weeks ago by
dbsgtk
• 0
0
votes
0
replies
14
views
Spam:
CBD Cream Boxes by BoxesGen & Custom Boxes Lab
mouse430a2.db
Cepo
6 weeks ago
hiraboxesgen
0
3
votes
4
replies
1.0k
views
Issue loading and downloading Bioconductor 3.22 packages after update
VariantAnnotation
Bioconductor
SNPlocs.Hsapiens.dbSNP155.GRCh38
6 weeks ago
strawberry3
• 0
0
votes
3
replies
398
views
Reproducibility of code in various Bioconductor versions
VariantAnnotation
SNPlocs.Hsapiens.dbSNP155.GRCh38
dbSNP
GenomicRanges
updated 6 weeks ago by
Gordon Smyth
53k • written 6 weeks ago by
strawberry3
• 0
1
vote
3
replies
547
views
Question on processing compound protein groups in limpa
limpa
updated 4 weeks ago by
brianpeterson1210
• 0 • written 6 weeks ago by
J Kim
▴ 10
0
votes
1
reply
241
views
Signature for msVIPER from paired bulk RNAseq data
viper
Normalization
pair
updated 6 weeks ago by
Michael Love
43k • written 6 weeks ago by
Kryštof
• 0
3
votes
2
replies
372
views
Correct usage of limpa for protein input
limpa
written 6 weeks ago by
miro165sabo
• 0
0
votes
0
replies
235
views
News:
Registration for EuroBioC2026 is open!
Bioconductor
Conference
6 weeks ago
laurah ondari
• 0
5
votes
3
replies
486
views
Which preprocessing steps are needed before running limpa?
Normalization
limpa
updated 6 weeks ago by
Gordon Smyth
53k • written 7 weeks ago by
miro165sabo
• 0
3
votes
3
replies
455
views
Can sample-level weights be used when analysing GSVA scores in limma?
limma
7 weeks ago • updated 6 weeks ago
A.Barden
▴ 20
0
votes
3
replies
419
views
Questions about bacon QC and correction on EWAS results
bacon
written 12 weeks ago by
sup0903
• 0
0
votes
0
replies
14
views
Spam:
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mouse430a2.db
7 weeks ago
cyber
0
0
votes
0
replies
15
views
Spam:
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mouse430a2.db
7 weeks ago
cyber
0
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Comment: lmma for lumi- request for help design matrix/contrast matrix
by
atlnuilix
• 0
It sounds like you have set up a solid framework for analyzing your Illumina BeadChips (HumanWG6) data for 42 samples, using a factorial ti…
Answer: Pathview not mapping all gene names in diagram
by
Guido Hooiveld
★ 4.1k
AFAIK the most likely reason the boxes still show the EC codes is because there are no enzymes in the organism you are investigating that c…
Comment: DESeq2 Design for 2 Conditions
by
atlnuilix
• 0
For an RNA-seq experiment like this using DESeq2, where you have two conditions (control vs treated) across two time points (day 21 and day…
Comment: day-of-hybridisation variability
by
atlnuilix
• 0
For experiments involving Affymetrix chips, variability due to the day of hybridization can indeed affect results, especially when replicat…
Comment: DESeq2 + analysis question for design with uneven time point design
by
atlnuilix
• 0
It models the main effects of time, treatment, and their interaction, helping identify genes whose expression changes specifically due to t…
Votes
Answer: Longitudinal analysis in Limma
A: Limma fixed and random effects
Answer: Blocking vs duplicateCorrelation for unbalanced designs in limma
Answer: Diffbind using EdgeR
Comment: DESeq2 single factor multiple levels, log of ratio or ratio of log ?
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