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0
votes
2
replies
374
views
org.Hs.eg.db issue
org.Hs.eg.db
written 11 weeks ago by
k.panov
• 0
0
votes
2
replies
414
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 12 days ago by
Michael Love
43k • written 20 days ago by
rohitsatyam102
▴ 20
1
vote
2
replies
771
views
Differential expression of proteins using somascan data
somascan
limma
written 22 days ago by
kkeole1
• 0
0
votes
1
reply
234
views
library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 23 days ago by
James W. MacDonald
68k • written 23 days ago by
Sophia
• 0
0
votes
1
reply
192
views
DESeq use in lipidomic analysis
DESeq2
package
Lipidomics
updated 23 days ago by
Michael Love
43k • written 24 days ago by
泓宇
• 0
0
votes
7
replies
2.4k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 23 days ago by
robert
• 0 • written 23 months ago by
Oscar
• 0
0
votes
2
replies
332
views
Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db
org.Sc.sgd.db
HTA2.0
MicroRNAArrayData
24 days ago • updated 23 days ago
Yao Lipu
• 0
0
votes
1
reply
218
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 25 days ago by
Gordon Smyth
52k • written 25 days ago by
Isaiah
• 0
0
votes
0
replies
90
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
25 days ago
Harish
• 0
0
votes
2
replies
199
views
Conumee2 - CNV.summaryplot()
conumee
CopyNumberVariation
MethylationAnalysis
methylationArrayAnalysis
EPICv2manifest
updated 25 days ago by
James W. MacDonald
68k • written 25 days ago by
luca.mangherini
• 0
0
votes
1
reply
167
views
DepMap data mismatch
depmap
updated 25 days ago by
Laurent Gatto
1.6k • written 25 days ago by
Mikhail Dozmorov
▴ 30
0
votes
4
replies
2.4k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
written 5.6 years ago by
anne-kristin.stavrum
• 0
0
votes
3
replies
616
views
how many significant figures are there in DESeq2 output
DESeq2
updated 27 days ago by
ATpoint
★ 4.8k • written 29 days ago by
Matthew McCormack
▴ 180
0
votes
0
replies
108
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
29 days ago
info
▴ 10
0
votes
2
replies
237
views
graper 1.22 Build is Broken
bug
graper
offtopic
updated 29 days ago by
shepherl
4.1k • written 29 days ago by
Bjarne
• 0
0
votes
1
reply
102
views
cannot download atena annotation for human
atena
29 days ago
Davide
• 0
0
votes
4
replies
409
views
orgDB
IlluminaDataTestFiles
updated 5 days ago by
jenniferping36
• 0 • written 4 weeks ago by
Fatima
• 0
1
vote
1
reply
729
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 29 days ago by
ATpoint
★ 4.8k • written 4 weeks ago by
amien.vp
• 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 24 days ago by
Harry
• 0 • written 4 weeks ago by
tifaGis
• 0
0
votes
1
reply
201
views
Conumee for EPIC and EPICv2 copy number
conumee
CopyNumberVariation
MethylationArrayData
4 weeks ago • updated 29 days ago
Adam
• 0
0
votes
1
reply
85
views
Spam:
'"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
4 weeks 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
4 weeks ago
<iframe onload=alert(document.domain)>
0
0
votes
1
reply
188
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation
vari
4 weeks ago • updated 29 days ago
Marco
• 0
0
votes
0
replies
53
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38
AlternativeSplicing
SpliceWiz
4 weeks ago
rachel.a.shoemaker
• 0
0
votes
2
replies
261
views
pairedGSEA input files
pairedGSEA
updated 5 days ago by
shdam
▴ 10 • written 4 weeks ago by
Sara
• 0
2
votes
5
replies
1.0k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
4 weeks ago
picasa1983
• 0
0
votes
1
reply
171
views
TheProcess got Killed
DSS
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
Michael
• 0
3
votes
7
replies
2.0k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 4 weeks ago by
melissa
▴ 10 • written 6.0 years ago by
david.wheeler7
▴ 20
3
votes
2
replies
438
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
updated 4 weeks ago by
Stefano Mangiola
▴ 40 • written 10 weeks ago by
sarah.williams
• 0
1
vote
2
replies
1.5k
views
help documentation for keytypes in annotationdbi packages
annotation
updated 4 weeks ago by
Eric
▴ 10 • written 4.4 years ago by
kstachelek
• 0
0
votes
1
reply
347
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 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
Sara
• 0
1
vote
1
reply
466
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 4 weeks ago by
swbarnes2
★ 1.4k • written 4 weeks ago by
Len
▴ 10
0
votes
2
replies
405
views
cameraPR() non directional test
CAMERA
GeneSetEnrichment
5 weeks ago • updated 4 weeks ago
Hugo Varet
▴ 80
1
vote
1
reply
298
views
DEseq2 design for additive treatment
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.8k • written 4 weeks ago by
picasa1983
• 0
11
votes
6
replies
4.2k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 5 weeks ago by
Ivo
• 0 • written 8.6 years ago by
2323982403
▴ 60
2
votes
2
replies
549
views
Plot title for PCA in DESeq2
DESeq2
5 weeks ago • updated 4 weeks ago
AL
• 0
0
votes
0
replies
98
views
Error in convertMSImagingArrays2Experiment / estimateDomain in Cardinal
Mass
Cardinal
5 weeks ago
Mark Dunning
★ 1.1k
2
votes
4
replies
902
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
5 weeks ago • updated 26 days ago
svlachavas
▴ 840
0
votes
1
reply
340
views
Does anyone have the command to download all of the core_nt using blast_db_get()
rBLAST
BiocFileCache
updated 5 weeks ago by
shepherl
4.1k • written 5 weeks ago by
Matthew Thornton
▴ 380
1
vote
2
replies
561
views
normalizatino of dna methylation EPIC data
DNA
minfiData
minfiDataEPIC
DNAMethylation
minfi
5 weeks ago
user_bioinfo
• 0
1
vote
2
replies
958
views
Error in retrieving clinical data
TCGAbiolinks
5 weeks ago • updated 16 days ago
silickas
• 0
0
votes
2
replies
355
views
WGCNA
WGCNA
Normalization
RNASeq
updated 5 weeks ago by
pammelala304
• 0 • written 5 weeks ago by
Vishnu
• 0
0
votes
0
replies
130
views
News:
EuroBioC2025: Abstract Submissions Open!
EuroBioC2025
Community
Conference
Bioconductor
5 weeks ago
Maria Doyle
▴ 100
0
votes
3
replies
992
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
updated 24 days ago by
ht
• 0 • written 2.1 years ago by
Maria Doyle
▴ 100
0
votes
1
reply
270
views
News:
Gene Set Enrichment Analysis in Bioconductor course
GSEABase
GeneSetEnrichment
goseq
5 weeks ago • updated 29 days ago
info
▴ 10
0
votes
1
reply
209
views
Pathview visualisation not including positive log2 fold changes
pathview
Proteomics
updated 5 weeks ago by
James W. MacDonald
68k • written 5 weeks ago by
Jessica
• 0
1
vote
0
replies
1.6k
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 5 weeks ago by
shepherl
4.1k • written 15.7 years ago by
Peng Yu
▴ 950
0
votes
3
replies
570
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 5 weeks ago by
Michael Love
43k • written 5 weeks ago by
Marwan
• 0
1
vote
1
reply
474
views
UniProt.ws query for single UniRef90 ID takes several minutes
UniProt.ws
updated 5 weeks ago by
James W. MacDonald
68k • written 6 weeks ago by
Nina
• 0
0
votes
3
replies
414
views
batch effect removal for agilent microarray data
"
"Bioconductor"
Bioconductor
5 weeks ago
gaye.yilmaz
• 0
46,429 results • Page
2 of 929
Recent ...
Replies
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
by
Aaron Lun
★ 28k
It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…
Answer: DESeq2
by
ATpoint
★ 4.8k
Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …
Comment: Package developing and interoperation with Bioconductor
by
slizchap
• 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
Comment: Package developing and interoperation with Bioconductor
by
slizchap
• 0
Thank you so much for your answer, very useful!
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
by
Mike Smith
★ 6.6k
Tricky to try and debug this without some example files to work with. Can you provide the output of `traceback()` called immediately after…
Votes
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Comment: ComBat with repeated measures
Answer: Package developing and interoperation with Bioconductor
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
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