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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
9 minutes ago
Len
• 0
0
votes
2
replies
225
views
cameraPR() non directional test
CAMERA
GeneSetEnrichment
3 days ago • updated 4 hours ago
Hugo Varet
▴ 80
1
vote
1
reply
64
views
DEseq2 design for additive treatment
DESeq2
updated 3 hours ago by
ATpoint
★ 4.7k • written 20 hours ago by
picasa1983
• 0
11
votes
6
replies
4.0k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 1 day ago by
Ivo
• 0 • written 8.5 years ago by
2323982403
▴ 60
1
vote
1
reply
165
views
Plot title for PCA in DESeq2
DESeq2
updated 2 days ago by
ATpoint
★ 4.7k • written 2 days ago by
AL
• 0
0
votes
0
replies
41
views
Error in convertMSImagingArrays2Experiment / estimateDomain in Cardinal
Mass
Cardinal
3 days ago
Mark Dunning
★ 1.1k
1
vote
2
replies
360
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
4 days ago • updated 1 day ago
svlachavas
▴ 840
0
votes
1
reply
267
views
Does anyone have the command to download all of the core_nt using blast_db_get()
rBLAST
BiocFileCache
updated 3 days ago by
shepherl
4.1k • written 3 days ago by
Matthew Thornton
▴ 380
1
vote
2
replies
454
views
normalizatino of dna methylation EPIC data
DNA
minfiData
minfiDataEPIC
DNAMethylation
minfi
4 days ago
user_bioinfo
• 0
0
votes
0
replies
47
views
Error in retrieving clinical data
TCGAbiolinks
4 days ago
silickas
• 0
0
votes
2
replies
263
views
WGCNA
WGCNA
Normalization
RNASeq
updated 3 days ago by
pammelala304
• 0 • written 4 days ago by
Vishnu
• 0
0
votes
0
replies
56
views
News:
EuroBioC2025: Abstract Submissions Open!
EuroBioC2025
Community
Conference
Bioconductor
4 days ago
Maria Doyle
▴ 100
0
votes
2
replies
860
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
updated 4 days ago by
cirwin009
• 0 • written 24 months ago by
Maria Doyle
▴ 100
0
votes
0
replies
52
views
News:
Gene Set Enrichment Analysis in Bioconductor course
cola
5 days ago
info
▴ 10
0
votes
1
reply
141
views
Pathview visualisation not including positive log2 fold changes
pathview
Proteomics
updated 5 days ago by
James W. MacDonald
68k • written 5 days ago by
Jessica
• 0
1
vote
0
replies
1.6k
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 5 days ago by
shepherl
4.1k • written 15.6 years ago by
Peng Yu
▴ 950
0
votes
3
replies
452
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 3 days ago by
Michael Love
43k • written 5 days ago by
Marwan
• 0
1
vote
1
reply
407
views
UniProt.ws query for single UniRef90 ID takes several minutes
UniProt.ws
updated 6 days ago by
James W. MacDonald
68k • written 9 days ago by
Nina
• 0
0
votes
3
replies
352
views
batch effect removal for agilent microarray data
"
"Bioconductor"
Bioconductor
6 days ago • updated 4 days ago
gaye.yilmaz
• 0
0
votes
2
replies
519
views
Automatically install dependencies
Install
dependencies
biocmanager
updated 6 days ago by
shepherl
4.1k • written 9 days ago by
jessica.gillespie
• 0
0
votes
2
replies
1.1k
views
Spam:
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updated 7 days ago by
xihaxiw582
• 0 • written 17.1 years ago by
Allison Hoskins
10
0
votes
1
reply
382
views
SingleR with multiple single cell references
SingleR
scran
updated 8 days ago by
Aaron Lun
★ 28k • written 8 days ago by
maltethodberg
▴ 180
0
votes
0
replies
52
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
9 days ago
Muhammad
• 0
0
votes
1
reply
527
views
To count or not to count multi-overlapping reads?
RNA-Seq
featureCounts
Rsubread
updated 9 days ago by
Gordon Smyth
52k • written 10 days ago by
Arindam
▴ 80
0
votes
0
replies
44
views
Unable to restore chromosome sequence lengths or other metadata in BSgenome.Mfascicularis.NCBI.6.0
BSgenome.Mfascicularis.NCBI.6.0
9 days ago
Genevieve
• 0
1
vote
2
replies
995
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 9 days ago by
ATpoint
★ 4.7k • written 10 days ago by
ingrid.h
• 0
0
votes
0
replies
73
views
Job:
Research Software Engineer - Bioconductor tools for biological data science and AI
Bioconductor
10 days ago
Wolfgang Huber
★ 13k
0
votes
0
replies
35
views
Generating Biphasic Curves in Offline GR Metrics Package
GRmetrics
10 days ago
Jasmitha
• 0
3
votes
5
replies
1.0k
views
Overcoming confounding in batch effect correction
sva
BiologicalQuestion
11 days ago • updated 10 days ago
bbao
▴ 10
3
votes
2
replies
950
views
Store Matrix in DataFrame Cell
S4Vectors
12 days ago • updated 10 days ago
Dario Strbenac
★ 1.6k
0
votes
7
replies
2.1k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 22 months ago by
Oscar
• 0
0
votes
5
replies
569
views
For some reason I can't update BiocManager to 3.20
Bioconductor
updated 5 days ago by
shepherl
4.1k • written 12 days ago by
azm.ana2
• 0
0
votes
0
replies
6
views
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netresponse
hgu219.db
MantelCorr
IlluminaDataTestFiles
12 days ago
Abu
0
0
votes
0
replies
6
views
Spam:
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PhenoGeneRanker
BSgenome.Osativa.MSU.MSU7
mouse.db0
SIM
12 days ago
Abu
0
0
votes
0
replies
8
views
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Qtlizer
ropls
TransOmicsData
MethylSeekR
12 days ago
Abu
0
0
votes
0
replies
10
views
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proDA
org.Sc.sgd.db
TVTB
12 days ago
Abu
0
0
votes
0
replies
10
views
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JobPosting
customCMPdb
TransOmicsData
12 days ago
Abu
0
0
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0
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12
views
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GOTHiC
BubbleTree
PANR
12 days ago
Abu
0
0
votes
1
reply
141
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler
KEGG
12 days ago
Jessica
• 0
0
votes
0
replies
45
views
News:
GBCC2025 Abstract Submissions & Registration Now Open!
Community
Conference
GBCC2025
Bioconductor
12 days ago
Maria Doyle
▴ 100
0
votes
1
reply
132
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 13 days ago by
Michael Love
43k • written 17 days ago by
Sahil
• 0
0
votes
1
reply
292
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA
pickSoftThreshold
SignedNowick
updated 13 days ago by
ATpoint
★ 4.7k • written 21 days ago by
ddrummer0056
• 0
0
votes
1
reply
141
views
Error: lexical error: invalid char in json text (alevin-seurat)
tximpo
tximportData
alevinQC
updated 13 days ago by
ATpoint
★ 4.7k • written 17 days ago by
ptlsugam
• 0
0
votes
0
replies
56
views
Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq
cumulativesumscaling
updated 13 days ago by
James W. MacDonald
68k • written 16 days ago by
boone5jones
• 0
0
votes
0
replies
160
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf
minfiDataEPIC
MethylationArrayData
MethylationArray
EPICv2manifest
16 days ago
charlie.wright
• 0
0
votes
3
replies
461
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 13 days ago by
980linnet
• 0 • written 18 days ago by
Guilherme
• 0
0
votes
4
replies
413
views
Web accessibility of Bioconductor.org
website
Website
updated 12 days ago by
Sean Davis
21k • written 18 days ago by
lizhare
• 0
1
vote
2
replies
744
views
Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = IntersectionNotEmpty)
GenomicAlignments
summarizeOverlaps(
Smart-seq2
proteinvariantcounting
19 days ago • updated 18 days ago
SofieK
• 0
0
votes
2
replies
270
views
Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis
Normalization
Epigenetics
MethylationArrayData
19 days ago
a.alkema
• 0
0
votes
2
replies
344
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 16 days ago by
Blair
• 0 • written 21 days ago by
A
• 0
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Answer: cameraPR() non directional test
by
Hugo Varet
▴ 80
Dear Gordon, thank you for your answer, that's exactly what I wanted to know. Happy to see you'll make it available in the next version o…
Answer: DEseq2 design for additive treatment
by
ATpoint
★ 4.7k
See https://support.bioconductor.org/p/69104/#69197, https://support.bioconductor.org/p/129755/ for testing against an average. Many other …
Comment: Use of limma R package with targeted proteomics for DE analysis
by
svlachavas
▴ 840
Dear Gordon, thanks a million for your reply (just saw it, did not get any notification through email) !! Regarding the log2 transformation…
Answer: cameraPR() non directional test
by
Gordon Smyth
52k
Yes, you can still do non-directional tests using cameraPR(), but it's not quite as easy as it was using the original camera() function as …
Answer: WGCNA with paired samples
by
Ivo
• 0
You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …
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Answer: DEseq2 design for additive treatment
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
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