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0
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2
replies
647
views
org.Hs.eg.db issue
org.Hs.eg.db
written 11 months ago by
k.panov
• 0
0
votes
2
replies
747
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 8 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
652
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
465
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
593
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
451
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 9 months ago by
Gordon Smyth
53k • written 9 months ago by
Isaiah
• 0
0
votes
0
replies
372
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
9 months ago
Harish
• 0
0
votes
2
replies
669
views
Conumee2 - CNV.summaryplot()
conumee
CopyNumberVariation
MethylationAnalysis
methylationArrayAnalysis
EPICv2manifest
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
luca.mangherini
• 0
0
votes
1
reply
377
views
DepMap data mismatch
depmap
updated 9 months ago by
Laurent Gatto
1.6k • written 9 months ago by
Mikhail Dozmorov
▴ 30
0
votes
4
replies
2.8k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
written 6.3 years ago by
anne-kristin.stavrum
• 0
0
votes
3
replies
993
views
how many significant figures are there in DESeq2 output
DESeq2
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
Matthew McCormack
▴ 180
0
votes
0
replies
354
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
9 months ago
info
▴ 10
0
votes
2
replies
527
views
graper 1.22 Build is Broken
bug
graper
offtopic
updated 9 months ago by
shepherl
4.2k • written 9 months ago by
Bjarne
• 0
0
votes
4
replies
767
views
orgDB
IlluminaDataTestFiles
updated 8 months ago by
jenniferping36
• 0 • written 9 months ago by
Fatima
• 0
1
vote
1
reply
2.0k
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 9 months ago by
ATpoint
★ 5.0k • written 9 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 9 months ago by
tifaGis
• 0
0
votes
1
reply
494
views
Conumee for EPIC and EPICv2 copy number
conumee
CopyNumberVariation
MethylationArrayData
9 months ago
Adam
• 0
0
votes
1
reply
86
views
Spam:
'"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
9 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
9 months ago
<iframe onload=alert(document.domain)>
0
0
votes
1
reply
387
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation
vari
9 months ago
Marco
• 0
0
votes
0
replies
291
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38
AlternativeSplicing
SpliceWiz
9 months ago
rachel.a.shoemaker
• 0
0
votes
2
replies
480
views
pairedGSEA input files
pairedGSEA
updated 8 months ago by
shdam
▴ 10 • written 9 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
9 months ago
picasa1983
• 0
0
votes
1
reply
362
views
TheProcess got Killed
DSS
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Michael
• 0
3
votes
7
replies
2.4k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 9 months ago by
melissa
▴ 10 • written 6.7 years ago by
david.wheeler7
▴ 20
3
votes
2
replies
794
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
updated 9 months ago by
Stefano Mangiola
▴ 40 • written 10 months ago by
sarah.williams
• 0
1
vote
2
replies
1.9k
views
help documentation for keytypes in annotationdbi packages
annotation
updated 9 months ago by
Eric
▴ 10 • written 5.1 years ago by
kstachelek
• 0
0
votes
1
reply
882
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 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Sara
• 0
1
vote
1
reply
653
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 9 months ago by
swbarnes2
★ 1.4k • written 9 months ago by
Len
▴ 10
0
votes
2
replies
692
views
cameraPR() non directional test
CAMERA
GeneSetEnrichment
9 months ago
Hugo Varet
▴ 80
1
vote
1
reply
451
views
DEseq2 design for additive treatment
DESeq2
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
picasa1983
• 0
11
votes
6
replies
4.8k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 9 months ago by
Ivo
• 0 • written 9.3 years ago by
2323982403
▴ 60
2
votes
2
replies
823
views
Plot title for PCA in DESeq2
DESeq2
9 months ago
AL
• 0
0
votes
0
replies
243
views
Error in convertMSImagingArrays2Experiment / estimateDomain in Cardinal
Mass
Cardinal
9 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
9 months ago
svlachavas
▴ 840
0
votes
1
reply
580
views
Does anyone have the command to download all of the core_nt using blast_db_get()
rBLAST
BiocFileCache
updated 9 months ago by
shepherl
4.2k • written 9 months ago by
Matthew Thornton
▴ 390
1
vote
2
replies
827
views
normalizatino of dna methylation EPIC data
DNA
minfiData
minfiDataEPIC
DNAMethylation
minfi
9 months ago
user_bioinfo
• 0
1
vote
2
replies
1.5k
views
Error in retrieving clinical data
TCGAbiolinks
9 months ago
silickas
• 0
0
votes
0
replies
546
views
News:
EuroBioC2025: Abstract Submissions Open!
EuroBioC2025
Community
Conference
Bioconductor
9 months ago
Maria Doyle
▴ 110
0
votes
1
reply
803
views
News:
Gene Set Enrichment Analysis in Bioconductor course
GSEABase
GeneSetEnrichment
goseq
9 months ago
info
▴ 10
0
votes
1
reply
426
views
Pathview visualisation not including positive log2 fold changes
pathview
Proteomics
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Jessica
• 0
1
vote
0
replies
1.8k
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 9 months ago by
shepherl
4.2k • written 16.4 years ago by
Peng Yu
▴ 950
0
votes
3
replies
1.0k
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 9 months ago by
Michael Love
43k • written 9 months ago by
Marwan
• 0
1
vote
1
reply
661
views
UniProt.ws query for single UniRef90 ID takes several minutes
UniProt.ws
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Nina
• 0
0
votes
3
replies
679
views
batch effect removal for agilent microarray data
"
"Bioconductor"
Bioconductor
9 months ago
gaye.yilmaz
• 0
0
votes
2
replies
1.2k
views
Automatically install dependencies
Install
dependencies
biocmanager
updated 9 months ago by
shepherl
4.2k • written 9 months ago by
jessica.gillespie
• 0
0
votes
2
replies
1.1k
views
Spam:
Welcome Bonus of USD 999 for free, join today!
updated 9 months ago by
xihaxiw582
• 0 • written 17.9 years ago by
Allison Hoskins
10
2
votes
2
replies
1.0k
views
SingleR with multiple single cell references
SingleR
scran
9 months ago • updated 8 months ago
maltethodberg
▴ 180
0
votes
0
replies
412
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
9 months ago
Muhammad
• 0
46,692 results • Page
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Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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