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Views
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1
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2
replies
104
views
Limma-voom sample weights and impact on DEG numbers
limma
written 3 days ago by
A.Barden
▴ 20
0
votes
1
reply
83
views
wgcna module preseravtion taking too long?
WGCNA
updated 3 days ago by
ATpoint
★ 5.0k • written 10 days ago by
lamia11me
• 0
0
votes
1
reply
176
views
Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCPlus)
HiC
HiCDCPlus
written 17 days ago by
Chaoability
• 0
0
votes
3
replies
144
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
written 6 days ago by
ja569116
• 0
0
votes
6
replies
2.5k
views
Ensembl site unresponsive via biomaRt
biomaRt
written 9 months ago by
hebda
• 0
0
votes
3
replies
174
views
segfault in edgeR glmQLFit
edgeR
updated 3 days ago by
Gordon Smyth
53k • written 6 days ago by
Mark
• 0
0
votes
3
replies
271
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 6 days ago by
Gordon Smyth
53k • written 8 days ago by
Durian
• 0
0
votes
0
replies
56
views
News:
Opportunity to host EuroBioC2026 Preconference workshops!
Conference
Workshop
Bioconductor
9 days ago
laurah ondari
• 0
0
votes
0
replies
69
views
Clarification on counting in Rsubread (featureCounts)
featureCounts
Rsubread
11 days ago • updated 3 days ago
Luca
• 0
0
votes
1
reply
119
views
NUPOP usage
TOAST
updated 15 days ago by
shepherl
4.2k • written 15 days ago by
Mohammad
• 0
1
vote
2
replies
278
views
News:
Important: Bioconductor Release 3.22 Delayed
release
written 8 weeks ago by
shepherl
4.2k
0
votes
2
replies
220
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 21 days ago by
Michael Love
43k • written 22 days ago by
Benjamin
• 0
0
votes
1
reply
177
views
PTM analysis in LIMPA
limpa
updated 21 days ago by
Gordon Smyth
53k • written 22 days ago by
Diego FGR
• 0
1
vote
0
replies
182
views
News:
Upcoming Ensembl API and data access changes - new blog post available
ensembl
mart
biomaRt
ensembldb
24 days ago
Ensembl_Jorge
▴ 10
0
votes
2
replies
211
views
problem reading bam files into nucleR
nucleR
updated 24 days ago by
James W. MacDonald
68k • written 28 days ago by
efoss
▴ 10
0
votes
0
replies
14
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
24 days ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
TOAST
24 days ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
24 days ago
Maya
0
0
votes
0
replies
8
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
24 days ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
24 days ago
Maya
0
3
votes
6
replies
908
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 5 weeks ago by
Ahmed Salah
• 0
0
votes
1
reply
1.3k
views
two questions about limma
Microarray
limma
Microarray
limma
updated 26 days ago by
Gordon Smyth
53k • written 18.8 years ago by
De-Jian ZHAO
▴ 240
0
votes
1
reply
165
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 26 days ago by
ATpoint
★ 5.0k • written 27 days ago by
Junmo
• 0
0
votes
1
reply
157
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
updated 4 days ago by
TikTsokaasocissalpc
• 0 • written 29 days ago by
laurah ondari
• 0
0
votes
1
reply
139
views
PFAM formats changed - is it still possible to use this with ISA?
IsoformSwitchAnalyzeR
updated 6 days ago by
TikTsokaasocissalpc
• 0 • written 4 weeks ago by
bolusharris
• 0
0
votes
2
replies
212
views
DECIPHER DesignProbes unable to design FISH-probes
decipher
FISH
DECIPHER
FISH-probe
probe-design
updated 2 days ago by
TikTsokaasocissalpc
• 0 • written 4 weeks ago by
vreinmuth
• 0
0
votes
2
replies
1.2k
views
p.adjust BH Question
written 14.3 years ago by
David Young
▴ 10
1
vote
4
replies
398
views
Large logFC but somewhat high FDR
limpa
4 weeks ago • updated 24 days ago
JKim
• 0
0
votes
1
reply
208
views
Job:
Bioinformatician at the Lausanne University Hospital
GenomicRanges
JobPosting
updated 2 days ago by
TikTsokaasocissalpc
• 0 • written 4 weeks ago by
story.benjamin
▴ 20
3
votes
5
replies
488
views
upstream git branches of bioc-release
Bioconductor
written 4 weeks ago by
Jeroen
▴ 10
0
votes
2
replies
181
views
limpa - drivers for unusually high standard error?
limpa
updated 4 weeks ago by
Gordon Smyth
53k • written 4 weeks ago by
Julia Broadbent
• 0
1
vote
4
replies
1.9k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
updated 13 days ago by
fnfgame
• 0 • written 7 months ago by
Franz Bachmann
• 0
0
votes
1
reply
419
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace
FlowCytometry
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Valeria
• 0
0
votes
2
replies
1.1k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Asma
• 0
0
votes
1
reply
390
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Sabina
• 0
0
votes
2
replies
377
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
luna.picello
• 0
0
votes
2
replies
446
views
BiocManager::install() doesn't work
Install
Biocond
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
flying_breadman
• 0
0
votes
2
replies
345
views
Results with PON give more variants
mutect2
variants
pon
written 5 months ago by
ramiro.barrantes
▴ 10
0
votes
1
reply
289
views
Empty boxes in treemap plot rrvgo package
rrvgo
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Asma
• 0
0
votes
1
reply
284
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek
CRISPR
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Citrus
• 0
0
votes
2
replies
475
views
Feedback needed on new user-friendly BED file tool
bedbaser
offtopic
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
nadia
• 0
0
votes
1
reply
274
views
sigDF object in sesame
sesame
sesameData
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Ramiro
• 0
0
votes
3
replies
388
views
Create consensusMatrix for codon bases
Biostrings
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Hassan
• 0
0
votes
2
replies
457
views
Memory error while running alignments
DECIPHER
Alignment
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Mihir
• 0
1
vote
11
replies
1.8k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Raya
• 0
0
votes
1
reply
282
views
Finding duplicated entries in GRangesList
GenomicRanges
updated 5 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Marco
• 0
0
votes
2
replies
311
views
DESeq2 on non-RNASeq counts data
DESeq2
updated 5 days ago by
TikTsokaasocissalpc
• 0 • written 4 months ago by
vs
• 0
0
votes
2
replies
475
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 25 days ago by
MarcHintz99
• 0 • written 3 months ago by
Rui
• 0
0
votes
1
reply
530
views
Problem with the TMB plot
Bioconductor
updated 5 weeks ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
nayanajose
• 0
0
votes
1
reply
304
views
mzR-Rcpp compiler version issue
Rcpp
Perseus
mzR
updated 5 weeks ago by
Laurent Gatto
1.6k • written 4 months ago by
bniego
• 0
1,000 results • Page
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Comment: nice 3D displays for PCA analysis
by
adam80haynes
• 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital
by
TikTsokaasocissalpc
• 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
TikTsokaasocissalpc
• 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Answer: wgcna module preseravtion taking too long?
by
ATpoint
★ 5.0k
WGCNA is not a Bioconductor package, you won't get an answer here. Consider biostars.org or the r/bioinformatics reddit. Note that 10 sampl…
Votes
Limma-voom sample weights and impact on DEG numbers
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
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