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Bile acid analysis with limpa
limpa
MassSpectrometry
MassSpectrometryData
updated 3 hours ago by
ATpoint
★ 5.0k • written 2 days ago by
DN
• 0
0
votes
0
replies
30
views
Changing multiple display parameters of a specific exon in GeneRegionTrack
Gviz
3 days ago
Xenia
• 0
0
votes
0
replies
29
views
Justify title track when rotation = 0
Gviz
gviz
3 days ago
Xenia
• 0
0
votes
12
replies
449
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 15 hours ago by
Gordon Smyth
53k • written 3 days ago by
chp265
• 0
0
votes
1
reply
222
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage
DESeq2
contrast
updated 4 days ago by
ATpoint
★ 5.0k • written 7 days ago by
ja569116
• 0
1
vote
3
replies
244
views
limpa analysis advice
limpa
updated 5 days ago by
Gordon Smyth
53k • written 8 days ago by
SamGG
▴ 360
0
votes
0
replies
58
views
News:
The BioC2026 Sticker Design Contest is Open!
Bioconductor
Conference
8 days ago
laurah ondari
• 0
0
votes
7
replies
404
views
limpa-blank normalization and Spectronaut's PTM stoichiometry
limpa
updated 2 days ago by
Gordon Smyth
53k • written 10 days ago by
emily.wolfrum
• 0
0
votes
2
replies
189
views
Are individual-mouse-based statistics possible in CellChat?
Bioconductor
CellChat
updated 8 hours ago by
LillianaVolkman99
• 0 • written 10 days ago by
Omer
• 0
4
votes
2
replies
241
views
When to use edgeR or limma
edgeR
limma
updated 7 days ago by
Gordon Smyth
53k • written 10 days ago by
abzhang97
• 0
0
votes
1
reply
87
views
Questions about bacon QC and correction on EWAS results
bacon
10 days ago
sup0903
• 0
3
votes
4
replies
255
views
Question about the filterByExpr function inputs in edgeR
RNASeq
filter
design
edgeR
model.matrix
10 days ago • updated 9 days ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
103
views
Development of MSstat workflow to analyze DIA time series data
MSstats
updated 10 days ago by
Gordon Smyth
53k • written 10 days ago by
sithurandi
• 0
0
votes
0
replies
123
views
MSstatsPTM-SpectronauttoMSstatsPTMFormat-failing with TAIR10 Locus Tags: Issue with UniProt-centric protein ID parsing
Bioconductor
MSstatsPTM
11 days ago
srkingwu
• 0
0
votes
0
replies
64
views
Junction CPM via Snapcount and Recount3
snapcount
recount3
11 days ago
henry.tietz
• 0
0
votes
0
replies
61
views
News:
Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano
GSEABase
pheatmap
Workshop
DESeq2
11 days ago
Frances Turner
▴ 20
0
votes
1
reply
87
views
How to convert .raw data for use in xcms
xcms
written 12 days ago by
Monica
• 0
0
votes
0
replies
141
views
Job:
Open Positions for Doctoral Researchers in Molecular Medicine
JobPosting
12 days ago
rubina.tabassum
• 0
1
vote
3
replies
187
views
Incosistencies in buildSNNGraph() function
scran
seurat
written 13 days ago by
Lucas
• 0
1
vote
0
replies
99
views
News:
Bioconductor Maintainer Application
maintainer
policy
Bioconductor
Devel
devel
14 days ago
shepherl
4.3k
0
votes
2
replies
261
views
Combining two proteomics datasets with limpa
limpa
ProteomicsWorkflow
limma
16 days ago • updated 2 days ago
Andrew Pattison
• 0
0
votes
0
replies
134
views
Job:
Jobs at Ensembl
ensembldb
18 days ago
Aleena_Ensembl
▴ 30
0
votes
0
replies
11
views
Spam:
Is there a way to map Excel fields to VCF contacts for accurate conversion?
ComputationalChemistry
Technology
Software
Website
updated 18 days ago by
shepherl
4.3k • written 18 days ago by
witebir963
0
0
votes
0
replies
83
views
Job:
Job:Computational Biologist position at the University of Alabama at Birmingham
hiring
RNASeq
JobPosting
SingleCell
SpatialData
18 days ago
lianov
• 0
2
votes
3
replies
224
views
please provide a BibTeX citation for "Advanced Single-Cell Analysis with Bioconductor"
Bioconductor
written 19 days ago by
Victor
▴ 10
2
votes
4
replies
231
views
Converting Probe IDs to HGNC symbols
Annotation
biomaRt
GEOquery
written 21 days ago by
Manav
▴ 10
0
votes
3
replies
285
views
How to do differential expresion across time serise with edgeR?
edgeR
timecoursedata
updated 20 days ago by
Gordon Smyth
53k • written 21 days ago by
petergrahamclark
▴ 10
1
vote
1
reply
223
views
How to install packages such as TCGAbiolinks, SumarizedExperiment?
TCGAbiolinks
SummarizedExperiment
updated 23 days ago by
Gordon Smyth
53k • written 23 days ago by
NewRUser
• 0
2
votes
3
replies
454
views
Guitar R package requires update due to dependency GenomicFeatures
GenomicFeatures
Guitar
txdbmaker
GenomicRanges
written 26 days ago by
ferran.llobet.cabau
▴ 10
0
votes
2
replies
181
views
ATACseq rudimentary questions
ATACSeq
DiffBind
27 days ago • updated 21 days ago
4747
• 0
4
votes
2
replies
405
views
Limma-voom sample weights and impact on DEG numbers
limma
4 weeks ago • updated 19 days ago
A.Barden
▴ 20
0
votes
3
replies
340
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
5 weeks ago • updated 7 days ago
ja569116
• 0
0
votes
3
replies
296
views
segfault in edgeR glmQLFit
edgeR
updated 4 weeks ago by
Gordon Smyth
53k • written 5 weeks ago by
Mark
• 0
0
votes
4
replies
604
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 18 days ago by
jtsy6383
• 0 • written 5 weeks ago by
Durian
• 0
0
votes
1
reply
269
views
News:
Opportunity to host EuroBioC2026 Preconference workshops!
Conference
Workshop
Bioconductor
written 5 weeks ago by
laurah ondari
• 0
0
votes
1
reply
270
views
wgcna module preseravtion taking too long?
WGCNA
updated 4 weeks ago by
ATpoint
★ 5.0k • written 5 weeks ago by
lamia11me
• 0
3
votes
4
replies
371
views
Clarification on counting in Rsubread (featureCounts)
featureCounts
Rsubread
updated 10 days ago by
Gordon Smyth
53k • written 5 weeks ago by
Luca
• 0
0
votes
1
reply
166
views
NUPOP usage
TOAST
updated 6 weeks ago by
shepherl
4.3k • written 6 weeks ago by
Mohammad
• 0
0
votes
1
reply
356
views
Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCPlus)
HiC
HiCDCPlus
written 6 weeks ago by
Chaoability
• 0
0
votes
1
reply
244
views
PTM analysis in LIMPA
limpa
updated 8 days ago by
Gordon Smyth
53k • written 7 weeks ago by
Diego FGR
• 0
0
votes
6
replies
562
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 4 days ago by
Martin Morgan
25k • written 7 weeks ago by
Benjamin
• 0
1
vote
1
reply
366
views
News:
Upcoming Ensembl API and data access changes - new blog post available
ensembl
mart
biomaRt
ensembldb
updated 1 day ago by
Hugo Gruson
• 0 • written 7 weeks ago by
Ensembl_Jorge
▴ 10
0
votes
0
replies
14
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
7 weeks ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
TOAST
7 weeks ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
7 weeks ago
Maya
0
0
votes
0
replies
8
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
7 weeks ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
7 weeks ago
Maya
0
0
votes
1
reply
225
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 7 weeks ago by
ATpoint
★ 5.0k • written 7 weeks ago by
Junmo
• 0
0
votes
2
replies
288
views
problem reading bam files into nucleR
nucleR
updated 7 weeks ago by
James W. MacDonald
68k • written 8 weeks ago by
efoss
▴ 10
0
votes
1
reply
338
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
written 8 weeks ago by
laurah ondari
• 0
46,730 results • Page
1 of 935
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Comment: Bile acid analysis with limpa
by
ATpoint
★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help
by
Jeremy
• 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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