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bioconductor
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26
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Are individual-mouse-based statistics possible in CellChat?
Bioconductor
CellChat
1 day ago
Omer
• 0
0
votes
0
replies
59
views
MSstatsPTM-SpectronauttoMSstatsPTMFormat-failing with TAIR10 Locus Tags: Issue with UniProt-centric protein ID parsing
Bioconductor
MSstatsPTM
2 days ago
srkingwu
• 0
1
vote
0
replies
70
views
News:
Bioconductor Maintainer Application
maintainer
policy
Bioconductor
Devel
devel
6 days ago
shepherl
4.3k
0
votes
1
reply
320
views
News:
Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
written 6 months ago by
Wei Shi
★ 3.6k
2
votes
3
replies
182
views
please provide a BibTeX citation for "Advanced Single-Cell Analysis with Bioconductor"
Bioconductor
written 10 days ago by
Victor
▴ 10
0
votes
1
reply
230
views
News:
Opportunity to host EuroBioC2026 Preconference workshops!
Conference
Workshop
Bioconductor
written 29 days ago by
laurah ondari
• 0
0
votes
1
reply
307
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
written 7 weeks ago by
laurah ondari
• 0
3
votes
5
replies
549
views
upstream git branches of bioc-release
Bioconductor
written 7 weeks ago by
Jeroen
▴ 10
0
votes
1
reply
438
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 7 weeks ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Sabina
• 0
0
votes
2
replies
503
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 6 weeks ago by
MarcHintz99
• 0 • written 4 months ago by
Rui
• 0
0
votes
2
replies
610
views
Problem with the TMB plot
Bioconductor
written 3 months ago by
nayanajose
• 0
2
votes
3
replies
568
views
DESeq2 design for haplotype MPRA
Bioconductor
written 3 months ago by
Rita
• 0
0
votes
0
replies
327
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
updated 8 weeks ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
jalte.jelsing
• 0
0
votes
2
replies
245
views
Alternative to BrainArray custom CDF packages for Affymetrix chips?
Bioconductor
updated 8 weeks ago by
Guido Hooiveld
★ 4.1k • written 8 weeks ago by
Stephen Piccolo
▴ 600
1
vote
0
replies
117
views
News:
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Bioconductor
8 weeks ago
Maria Doyle
▴ 110
0
votes
2
replies
342
views
featureCounts -L: high unassigned:mapq fraction
Bioconductor
written 3 months ago by
sikora
• 0
1
vote
2
replies
474
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment
edgeR
miloR
Bioconductor
updated 9 weeks ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Joseph
• 0
1
vote
2
replies
449
views
incomplete imputation of missing values with LEA impute() function
Bioconductor
LEA
updated 9 weeks ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
nadia
• 0
2
votes
2
replies
590
views
What R/Bioconductor tools would you recommend for the analysis of sncRNA, specifically piRNA?
Bioconductor
3 months ago • updated 9 weeks ago
Matthew Thornton
▴ 390
0
votes
3
replies
313
views
Integration: Paired-end vs healthy single-end from a different source
Bioconductor
written 10 weeks ago by
m.c.ruma
• 0
1
vote
4
replies
453
views
"Watched Tags" are being erased rather than updated
Bioconductor
updated 8 weeks ago by
RalphSavage99
• 0 • written 11 weeks ago by
jessica.anderson
▴ 10
0
votes
1
reply
256
views
Question about collapsing ASVs by genus level during DESeq2 analysis
Bioconductor
updated 10 weeks ago by
Michael Love
43k • written 3 months ago by
acharyapratiksha24
• 0
0
votes
7
replies
2.2k
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
written 2.9 years ago by
Maria Doyle
▴ 110
0
votes
0
replies
12
views
Spam:
The Neon Code PolyTrack
Bioconductor
10 weeks ago
residentialplayt
0
2
votes
1
reply
532
views
News:
Bioconductor 3.22 Released!
release
Release
Bioconductor
Software
written 11 weeks ago by
shepherl
4.3k
0
votes
1
reply
458
views
News:
Save the Date: BioC2026
Bioconductor
written 11 weeks ago by
shepherl
4.3k
0
votes
3
replies
277
views
Using DESeq2 for age prediction
Bioconductor
updated 11 weeks ago by
ATpoint
★ 5.0k • written 11 weeks ago by
picasa1983
• 0
4
votes
3
replies
643
views
DESeq2 for candidate gene analysis
Bioconductor
written 3 months ago by
piffelpaff
▴ 20
0
votes
3
replies
335
views
"organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
Bioconductor
3 months ago
ubjw24
• 0
0
votes
3
replies
473
views
NA values for DESeq2 p-values and adjusted p-values using large sample sizes
Bioconductor
3 months ago
Gabriel
• 0
0
votes
1
reply
190
views
Gatins Set error
flowCore
Bioconductor
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
yoav.lubelsky
• 0
0
votes
1
reply
259
views
Job:
Senior Teaching Fellow (MSc Computational Biomedicine)
Bioconductor
written 3 months ago by
s.samarajiwa
• 0
0
votes
1
reply
729
views
News:
Bioconductor 3.22 Release Schedule
Devel
Release
Bioconductor
written 4 months ago by
shepherl
4.3k
1
vote
2
replies
377
views
Error Loading Experiment from SimBenchData Package
Bioconductor
3 months ago
ksankaran
• 0
0
votes
3
replies
386
views
Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 3 months ago by
Aaron Lun
★ 29k • written 3 months ago by
Stephen Piccolo
▴ 600
0
votes
6
replies
595
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 3 months ago by
James W. MacDonald
68k • written 4 months ago by
Skyler
• 0
0
votes
1
reply
225
views
Job:
Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
written 4 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
402
views
News:
Bioconductor Board Nominations Open
TAB
Bioconductor
CAB
written 6 months ago by
shepherl
4.3k
0
votes
3
replies
2.5k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma
Bioconductor
Metabolomics
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
anni
• 0
0
votes
2
replies
1.1k
views
Starting with a clean bioconductor rstudio container
Bioconductor
updated 6 months ago by
ATpoint
★ 5.0k • written 7 months ago by
Ramiro
• 0
0
votes
9
replies
13k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 7 months ago by
Hadi
• 0 • written 4.5 years ago by
charlotte
▴ 10
0
votes
0
replies
373
views
Job:
Lab Head positions at the WEHI, Melbourne, Australia
JobPosting
Bioconductor
7 months ago
Gordon Smyth
53k
0
votes
4
replies
9.2k
views
Bioconductor version cannot be validated
Bioconductor
Annotation
Ann
written 2.3 years ago by
Aytaç
• 0
0
votes
2
replies
612
views
GBCC2025: New Scholarship Opportunities Available!
Community
Conference
GBCC2025
Bioconductor
updated 4 months ago by
Liona
• 0 • written 7 months ago by
Maria Doyle
▴ 110
0
votes
1
reply
501
views
Best tximport quant.genes.sf
tximport
tximeta
Bioconductor
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
yob4003
• 0
0
votes
2
replies
861
views
Version conflict when pushing to scQTLtools devel branch
Bioconductor
written 9 months ago by
XFWu
• 0
1
vote
5
replies
1.9k
views
Package developing and interoperation with Bioconductor
Package
Bioconductor
written 9 months ago by
slizchap
• 0
0
votes
5
replies
2.8k
views
News:
EuroBioC2024 abstract submission is open!
Conference
Bioconductor
EuroBioC2024
written 23 months ago by
Maria Doyle
▴ 110
0
votes
1
reply
931
views
News:
List of Deprecated Packages for Bioc3.20
Release
Devel
Bioconductor
15 months ago • updated 9 months ago
shepherl
4.3k
0
votes
0
replies
625
views
News:
EuroBioC2025: Abstract Submissions Open!
EuroBioC2025
Community
Conference
Bioconductor
10 months ago
Maria Doyle
▴ 110
915 results • Page
1 of 19
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Replies
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Noted, thank you very much.
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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