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Bioconductor
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Chip Seq Analysis of RNA Polymerase 2
ChIPseeker
ChIPSeqData
ChIPSeq
Bioconductor
written 10 days ago by
Gaurav
• 0
0
votes
1
reply
229
views
News:
The Call for Abstracts for BioC2026 is open!
Bioconductor
Conference
written 11 days ago by
laurah ondari
• 0
0
votes
1
reply
2.6k
views
Tutorial:
[LIBD rstats club] Bioconductor overview
bioconductor
libdrstats
Tutorial
written 5.8 years ago by
Leonardo Collado Torres
★ 1.1k
0
votes
0
replies
152
views
News:
Deadline Extended: EuroBioC2026 Call for Abstracts
Bioconductor
Conference
15 days ago
laurah ondari
• 0
0
votes
2
replies
337
views
Are individual-mouse-based statistics possible in CellChat?
Bioconductor
CellChat
updated 21 days ago by
LillianaVolkman99
• 0 • written 4 weeks ago by
Omer
• 0
0
votes
1
reply
170
views
News:
The BioC2026 Sticker Design Contest is Open!
Bioconductor
Conference
written 29 days ago by
laurah ondari
• 0
0
votes
0
replies
384
views
MSstatsPTM-SpectronauttoMSstatsPTMFormat-failing with TAIR10 Locus Tags: Issue with UniProt-centric protein ID parsing
Bioconductor
MSstatsPTM
4 weeks ago
srkingwu
• 0
1
vote
1
reply
199
views
News:
Bioconductor Maintainer Application
maintainer
policy
Bioconductor
Devel
devel
written 5 weeks ago by
shepherl
4.3k
0
votes
1
reply
483
views
News:
Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
written 7 months ago by
Wei Shi
★ 3.6k
2
votes
3
replies
267
views
please provide a BibTeX citation for "Advanced Single-Cell Analysis with Bioconductor"
Bioconductor
written 5 weeks ago by
Victor
▴ 10
0
votes
1
reply
336
views
News:
Opportunity to host EuroBioC2026 Preconference workshops!
Conference
Workshop
Bioconductor
written 8 weeks ago by
laurah ondari
• 0
0
votes
1
reply
418
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
written 11 weeks ago by
laurah ondari
• 0
3
votes
5
replies
608
views
upstream git branches of bioc-release
Bioconductor
written 11 weeks ago by
Jeroen
▴ 10
0
votes
1
reply
480
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Sabina
• 0
0
votes
2
replies
580
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 10 weeks ago by
MarcHintz99
• 0 • written 5 months ago by
Rui
• 0
0
votes
2
replies
719
views
Problem with the TMB plot
Bioconductor
written 4 months ago by
nayanajose
• 0
2
votes
3
replies
631
views
DESeq2 design for haplotype MPRA
Bioconductor
written 4 months ago by
Rita
• 0
0
votes
0
replies
365
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
jalte.jelsing
• 0
0
votes
2
replies
340
views
Alternative to BrainArray custom CDF packages for Affymetrix chips?
Bioconductor
updated 12 weeks ago by
Guido Hooiveld
★ 4.1k • written 3 months ago by
Stephen Piccolo
▴ 600
1
vote
0
replies
162
views
News:
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Bioconductor
3 months ago
Maria Doyle
▴ 110
0
votes
2
replies
406
views
featureCounts -L: high unassigned:mapq fraction
Bioconductor
written 4 months ago by
sikora
• 0
1
vote
2
replies
543
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment
edgeR
miloR
Bioconductor
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Joseph
• 0
1
vote
2
replies
534
views
incomplete imputation of missing values with LEA impute() function
Bioconductor
LEA
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
nadia
• 0
2
votes
2
replies
683
views
What R/Bioconductor tools would you recommend for the analysis of sncRNA, specifically piRNA?
Bioconductor
4 months ago • updated 3 months ago
Matthew Thornton
▴ 390
0
votes
3
replies
334
views
Integration: Paired-end vs healthy single-end from a different source
Bioconductor
written 3 months ago by
m.c.ruma
• 0
1
vote
4
replies
500
views
"Watched Tags" are being erased rather than updated
Bioconductor
updated 3 months ago by
RalphSavage99
• 0 • written 3 months ago by
jessica.anderson
▴ 10
0
votes
1
reply
278
views
Question about collapsing ASVs by genus level during DESeq2 analysis
Bioconductor
updated 3 months ago by
Michael Love
43k • written 4 months ago by
acharyapratiksha24
• 0
0
votes
7
replies
2.2k
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
written 3.0 years ago by
Maria Doyle
▴ 110
0
votes
0
replies
12
views
Spam:
The Neon Code PolyTrack
Bioconductor
3 months ago
residentialplayt
0
2
votes
1
reply
835
views
News:
Bioconductor 3.22 Released!
release
Release
Bioconductor
Software
written 3 months ago by
shepherl
4.3k
0
votes
1
reply
607
views
News:
Save the Date: BioC2026
Bioconductor
written 3 months ago by
shepherl
4.3k
0
votes
3
replies
304
views
Using DESeq2 for age prediction
Bioconductor
updated 3 months ago by
ATpoint
★ 5.0k • written 3 months ago by
picasa1983
• 0
4
votes
3
replies
665
views
DESeq2 for candidate gene analysis
Bioconductor
written 4 months ago by
piffelpaff
▴ 20
0
votes
3
replies
385
views
"organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
Bioconductor
4 months ago
ubjw24
• 0
0
votes
3
replies
526
views
NA values for DESeq2 p-values and adjusted p-values using large sample sizes
Bioconductor
4 months ago
Gabriel
• 0
0
votes
1
reply
217
views
Gatins Set error
flowCore
Bioconductor
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
yoav.lubelsky
• 0
0
votes
1
reply
286
views
Job:
Senior Teaching Fellow (MSc Computational Biomedicine)
Bioconductor
written 4 months ago by
s.samarajiwa
• 0
0
votes
1
reply
1.2k
views
News:
Bioconductor 3.22 Release Schedule
Devel
Release
Bioconductor
written 5 months ago by
shepherl
4.3k
1
vote
2
replies
401
views
Error Loading Experiment from SimBenchData Package
Bioconductor
4 months ago
ksankaran
• 0
0
votes
3
replies
454
views
Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 4 months ago by
Aaron Lun
★ 29k • written 4 months ago by
Stephen Piccolo
▴ 600
0
votes
6
replies
784
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 4 months ago by
James W. MacDonald
68k • written 5 months ago by
Skyler
• 0
0
votes
1
reply
246
views
Job:
Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
written 5 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
435
views
News:
Bioconductor Board Nominations Open
TAB
Bioconductor
CAB
written 7 months ago by
shepherl
4.3k
0
votes
3
replies
2.6k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma
Bioconductor
Metabolomics
updated 7 months ago by
Gordon Smyth
53k • written 7 months ago by
anni
• 0
0
votes
2
replies
1.1k
views
Starting with a clean bioconductor rstudio container
Bioconductor
updated 7 months ago by
ATpoint
★ 5.0k • written 8 months ago by
Ramiro
• 0
0
votes
9
replies
14k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 8 months ago by
Hadi
• 0 • written 4.5 years ago by
charlotte
▴ 10
0
votes
0
replies
400
views
Job:
Lab Head positions at the WEHI, Melbourne, Australia
JobPosting
Bioconductor
8 months ago
Gordon Smyth
53k
0
votes
4
replies
9.4k
views
Bioconductor version cannot be validated
Bioconductor
Annotation
Ann
written 2.4 years ago by
Aytaç
• 0
0
votes
2
replies
664
views
GBCC2025: New Scholarship Opportunities Available!
Community
Conference
GBCC2025
Bioconductor
updated 5 months ago by
Liona
• 0 • written 8 months ago by
Maria Doyle
▴ 110
0
votes
1
reply
591
views
Best tximport quant.genes.sf
tximport
tximeta
Bioconductor
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
yob4003
• 0
919 results • Page
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Replies
Comment: Which preprocessing steps are needed before running limpa?
by
miro165sabo
• 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
by
Gordon Smyth
53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Korneel
• 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics
by
yesquokkan
• 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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