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pairedGSEA input files
pairedGSEA
updated 9 months ago by
shdam
▴ 10 • written 10 months ago by
Sara
• 0
2
votes
5
replies
1.5k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
10 months ago
picasa1983
• 0
0
votes
1
reply
383
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
2.5k
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
831
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
updated 10 months ago by
Stefano Mangiola
▴ 40 • written 12 months ago by
sarah.williams
• 0
1
vote
2
replies
2.0k
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
1.1k
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
718
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
719
views
cameraPR() non directional test
CAMERA
GeneSetEnrichment
10 months ago
Hugo Varet
▴ 80
1
vote
1
reply
469
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
4.9k
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
889
views
Plot title for PCA in DESeq2
DESeq2
10 months ago
AL
• 0
0
votes
0
replies
279
views
Error in convertMSImagingArrays2Experiment / estimateDomain in Cardinal
Mass
Cardinal
10 months ago
Mark Dunning
★ 1.1k
2
votes
4
replies
1.6k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
10 months ago
svlachavas
▴ 840
0
votes
1
reply
628
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
4.3k • written 10 months ago by
Matthew Thornton
▴ 390
1
vote
2
replies
854
views
normalizatino of dna methylation EPIC data
DNA
minfiData
minfiDataEPIC
DNAMethylation
minfi
10 months ago
user_bioinfo
• 0
1
vote
2
replies
1.7k
views
Error in retrieving clinical data
TCGAbiolinks
10 months ago
silickas
• 0
0
votes
0
replies
622
views
News:
EuroBioC2025: Abstract Submissions Open!
EuroBioC2025
Community
Conference
Bioconductor
10 months ago
Maria Doyle
▴ 110
0
votes
1
reply
855
views
News:
Gene Set Enrichment Analysis in Bioconductor course
GSEABase
GeneSetEnrichment
goseq
10 months ago
info
▴ 10
0
votes
1
reply
467
views
Pathview visualisation not including positive log2 fold changes
pathview
Proteomics
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
Jessica
• 0
1
vote
0
replies
1.8k
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 10 months ago by
shepherl
4.3k • written 16.5 years ago by
Peng Yu
▴ 950
0
votes
3
replies
1.1k
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 10 months ago by
Michael Love
43k • written 10 months ago by
Marwan
• 0
1
vote
1
reply
710
views
UniProt.ws query for single UniRef90 ID takes several minutes
UniProt.ws
updated 10 months ago by
James W. MacDonald
68k • written 11 months ago by
Nina
• 0
0
votes
3
replies
724
views
batch effect removal for agilent microarray data
"
"Bioconductor"
Bioconductor
10 months ago
gaye.yilmaz
• 0
0
votes
2
replies
1.4k
views
Automatically install dependencies
Install
dependencies
biocmanager
updated 10 months ago by
shepherl
4.3k • written 11 months ago by
jessica.gillespie
• 0
0
votes
2
replies
1.1k
views
Spam:
Welcome Bonus of USD 999 for free, join today!
updated 11 months ago by
xihaxiw582
• 0 • written 18.0 years ago by
Allison Hoskins
10
2
votes
2
replies
1.1k
views
SingleR with multiple single cell references
SingleR
scran
11 months ago • updated 9 months ago
maltethodberg
▴ 180
0
votes
0
replies
431
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
11 months ago
Muhammad
• 0
0
votes
1
reply
1.1k
views
To count or not to count multi-overlapping reads?
RNA-Seq
featureCounts
Rsubread
updated 11 months ago by
Gordon Smyth
53k • written 11 months ago by
Arindam
▴ 80
0
votes
0
replies
245
views
Unable to restore chromosome sequence lengths or other metadata in BSgenome.Mfascicularis.NCBI.6.0
BSgenome.Mfascicularis.NCBI.6.0
11 months ago
Genevieve
• 0
1
vote
2
replies
1.4k
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
ingrid.h
• 0
0
votes
0
replies
648
views
Job:
Research Software Engineer - Bioconductor tools for biological data science and AI
Bioconductor
11 months ago
Wolfgang Huber
★ 13k
0
votes
0
replies
213
views
Generating Biphasic Curves in Offline GR Metrics Package
GRmetrics
11 months ago
Jasmitha
• 0
3
votes
5
replies
1.7k
views
Overcoming confounding in batch effect correction
sva
BiologicalQuestion
11 months ago
bbao
▴ 10
3
votes
2
replies
1.2k
views
Store Matrix in DataFrame Cell
S4Vectors
11 months ago
Dario Strbenac
★ 1.6k
0
votes
5
replies
2.3k
views
For some reason I can't update BiocManager to 3.20
Bioconductor
updated 10 months ago by
shepherl
4.3k • written 11 months ago by
azm.ana2
• 0
0
votes
0
replies
6
views
Spam:
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netresponse
hgu219.db
MantelCorr
IlluminaDataTestFiles
11 months ago
Abu
0
0
votes
0
replies
6
views
Spam:
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PhenoGeneRanker
BSgenome.Osativa.MSU.MSU7
mouse.db0
SIM
11 months ago
Abu
0
0
votes
0
replies
8
views
Spam:
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Qtlizer
ropls
TransOmicsData
MethylSeekR
11 months ago
Abu
0
0
votes
0
replies
10
views
Spam:
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proDA
org.Sc.sgd.db
TVTB
11 months ago
Abu
0
0
votes
0
replies
10
views
Spam:
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JobPosting
customCMPdb
TransOmicsData
11 months ago
Abu
0
0
votes
0
replies
12
views
Spam:
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GOTHiC
BubbleTree
PANR
11 months ago
Abu
0
0
votes
1
reply
818
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler
KEGG
11 months ago
Jessica
• 0
0
votes
0
replies
538
views
News:
GBCC2025 Abstract Submissions & Registration Now Open!
Community
Conference
GBCC2025
Bioconductor
11 months ago
Maria Doyle
▴ 110
0
votes
1
reply
462
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Sahil
• 0
0
votes
1
reply
839
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA
pickSoftThreshold
SignedNowick
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
ddrummer0056
• 0
0
votes
1
reply
458
views
Error: lexical error: invalid char in json text (alevin-seurat)
tximpo
tximportData
alevinQC
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
ptlsugam
• 0
0
votes
0
replies
244
views
Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq
cumulativesumscaling
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
boone5jones
• 0
0
votes
0
replies
374
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf
minfiDataEPIC
MethylationArrayData
MethylationArray
EPICv2manifest
11 months ago
charlie.wright
• 0
0
votes
3
replies
886
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 11 months ago by
980linnet
• 0 • written 11 months ago by
Guilherme
• 0
1,000 results • Page
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Comment: Development of MSstat workflow to analyze DIA time series data
by
Gordon Smyth
53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR
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53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
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Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
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There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
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A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
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