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BioConductor
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News:
Opportunity to host EuroBioC2026 Preconference workshops!
Conference
Workshop
Bioconductor
2 days ago
laurah ondari
• 0
0
votes
0
replies
81
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
22 days ago
laurah ondari
• 0
3
votes
5
replies
449
views
upstream git branches of bioc-release
Bioconductor
written 25 days ago by
Jeroen
▴ 10
0
votes
1
reply
373
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 27 days ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Sabina
• 0
0
votes
2
replies
455
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 18 days ago by
MarcHintz99
• 0 • written 3 months ago by
Rui
• 0
0
votes
1
reply
515
views
Problem with the TMB plot
Bioconductor
updated 28 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
nayanajose
• 0
2
votes
3
replies
513
views
DESeq2 design for haplotype MPRA
Bioconductor
written 9 weeks ago by
Rita
• 0
0
votes
0
replies
277
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
jalte.jelsing
• 0
0
votes
2
replies
194
views
Alternative to BrainArray custom CDF packages for Affymetrix chips?
Bioconductor
updated 4 weeks ago by
Guido Hooiveld
★ 4.1k • written 5 weeks ago by
Stephen Piccolo
▴ 600
1
vote
0
replies
83
views
News:
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Bioconductor
5 weeks ago
Maria Doyle
▴ 110
0
votes
2
replies
286
views
featureCounts -L: high unassigned:mapq fraction
Bioconductor
written 11 weeks ago by
sikora
• 0
1
vote
2
replies
447
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment
edgeR
miloR
Bioconductor
updated 5 weeks ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
Joseph
• 0
1
vote
2
replies
389
views
incomplete imputation of missing values with LEA impute() function
Bioconductor
LEA
updated 5 weeks ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
nadia
• 0
2
votes
2
replies
531
views
What R/Bioconductor tools would you recommend for the analysis of sncRNA, specifically piRNA?
Bioconductor
11 weeks ago • updated 5 weeks ago
Matthew Thornton
▴ 390
0
votes
3
replies
270
views
Integration: Paired-end vs healthy single-end from a different source
Bioconductor
written 6 weeks ago by
m.c.ruma
• 0
1
vote
4
replies
419
views
"Watched Tags" are being erased rather than updated
Bioconductor
updated 4 weeks ago by
RalphSavage99
• 0 • written 7 weeks ago by
jessica.anderson
▴ 10
0
votes
1
reply
239
views
Question about collapsing ASVs by genus level during DESeq2 analysis
Bioconductor
updated 6 weeks ago by
Michael Love
43k • written 10 weeks ago by
acharyapratiksha24
• 0
0
votes
7
replies
2.1k
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
written 2.8 years ago by
Maria Doyle
▴ 110
0
votes
0
replies
12
views
Spam:
The Neon Code PolyTrack
Bioconductor
7 weeks ago
residentialplayt
0
2
votes
1
reply
256
views
News:
Bioconductor 3.22 Released!
release
Release
Bioconductor
Software
written 7 weeks ago by
shepherl
4.2k
0
votes
1
reply
158
views
News:
Save the Date: BioC2026
Bioconductor
written 7 weeks ago by
shepherl
4.2k
0
votes
3
replies
257
views
Using DESeq2 for age prediction
Bioconductor
updated 7 weeks ago by
ATpoint
★ 5.0k • written 7 weeks ago by
picasa1983
• 0
4
votes
3
replies
618
views
DESeq2 for candidate gene analysis
Bioconductor
written 3 months ago by
piffelpaff
▴ 20
0
votes
3
replies
295
views
"organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
Bioconductor
9 weeks ago
ubjw24
• 0
0
votes
3
replies
441
views
NA values for DESeq2 p-values and adjusted p-values using large sample sizes
Bioconductor
11 weeks ago • updated 9 weeks ago
Gabriel
• 0
0
votes
1
reply
171
views
Gatins Set error
flowCore
Bioconductor
updated 11 weeks ago by
James W. MacDonald
68k • written 11 weeks ago by
yoav.lubelsky
• 0
0
votes
1
reply
235
views
Job:
Senior Teaching Fellow (MSc Computational Biomedicine)
Bioconductor
written 11 weeks ago by
s.samarajiwa
• 0
0
votes
1
reply
445
views
News:
Bioconductor 3.22 Release Schedule
Devel
Release
Bioconductor
written 3 months ago by
shepherl
4.2k
1
vote
2
replies
355
views
Error Loading Experiment from SimBenchData Package
Bioconductor
12 weeks ago • updated 10 weeks ago
ksankaran
• 0
0
votes
3
replies
352
views
Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 11 weeks ago by
Aaron Lun
★ 29k • written 12 weeks ago by
Stephen Piccolo
▴ 600
0
votes
6
replies
506
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
Skyler
• 0
0
votes
1
reply
205
views
Job:
Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
written 3 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
384
views
News:
Bioconductor Board Nominations Open
TAB
Bioconductor
CAB
written 5 months ago by
shepherl
4.2k
0
votes
0
replies
235
views
News:
Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
5 months ago
Wei Shi
★ 3.6k
0
votes
3
replies
2.4k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma
Bioconductor
Metabolomics
updated 5 months ago by
Gordon Smyth
53k • written 5 months ago by
anni
• 0
0
votes
2
replies
1.1k
views
Starting with a clean bioconductor rstudio container
Bioconductor
updated 5 months ago by
ATpoint
★ 5.0k • written 6 months ago by
Ramiro
• 0
0
votes
9
replies
13k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 6 months ago by
Hadi
• 0 • written 4.4 years ago by
charlotte
▴ 10
0
votes
0
replies
352
views
Job:
Lab Head positions at the WEHI, Melbourne, Australia
JobPosting
Bioconductor
6 months ago
Gordon Smyth
53k
0
votes
4
replies
8.9k
views
Bioconductor version cannot be validated
Bioconductor
Annotation
Ann
written 2.3 years ago by
Aytaç
• 0
0
votes
2
replies
584
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
474
views
Best tximport quant.genes.sf
tximport
tximeta
Bioconductor
updated 7 months ago by
ATpoint
★ 5.0k • written 7 months ago by
yob4003
• 0
0
votes
2
replies
839
views
Version conflict when pushing to scQTLtools devel branch
Bioconductor
written 8 months ago by
XFWu
• 0
1
vote
5
replies
1.8k
views
Package developing and interoperation with Bioconductor
Package
Bioconductor
written 8 months ago by
slizchap
• 0
0
votes
5
replies
2.7k
views
News:
EuroBioC2024 abstract submission is open!
Conference
Bioconductor
EuroBioC2024
written 22 months ago by
Maria Doyle
▴ 110
0
votes
1
reply
879
views
News:
List of Deprecated Packages for Bioc3.20
Release
Devel
Bioconductor
14 months ago • updated 8 months ago
shepherl
4.2k
0
votes
0
replies
567
views
News:
EuroBioC2025: Abstract Submissions Open!
EuroBioC2025
Community
Conference
Bioconductor
10 months ago
Maria Doyle
▴ 110
0
votes
3
replies
688
views
batch effect removal for agilent microarray data
"
"Bioconductor"
Bioconductor
10 months ago
gaye.yilmaz
• 0
0
votes
0
replies
615
views
Job:
Research Software Engineer - Bioconductor tools for biological data science and AI
Bioconductor
10 months ago
Wolfgang Huber
★ 13k
0
votes
5
replies
1.9k
views
For some reason I can't update BiocManager to 3.20
Bioconductor
updated 10 months ago by
shepherl
4.2k • written 10 months ago by
azm.ana2
• 0
0
votes
0
replies
502
views
News:
GBCC2025 Abstract Submissions & Registration Now Open!
Community
Conference
GBCC2025
Bioconductor
10 months ago
Maria Doyle
▴ 110
911 results • Page
1 of 19
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Replies
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
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 …
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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