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Development of MSstat workflow to analyze DIA time series data
MSstats
41 minutes ago
sithurandi
• 0
0
votes
0
replies
27
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MSstatsPTM-SpectronauttoMSstatsPTMFormat-failing with TAIR10 Locus Tags: Issue with UniProt-centric protein ID parsing
Bioconductor
MSstatsPTM
10 hours ago • updated 9 hours ago
srkingwu
• 0
8
votes
8
replies
2.8k
views
Confounded design, batch effect correction (edgeR)
rnaseq
edger
differential gene expression
batch effect
written 7.3 years ago by
Laura
▴ 20
0
votes
0
replies
27
views
Junction CPM via Snapcount and Recount3
snapcount
recount3
1 day ago
henry.tietz
• 0
3
votes
4
replies
225
views
Clarification on counting in Rsubread (featureCounts)
featureCounts
Rsubread
updated 40 minutes ago by
Gordon Smyth
53k • written 29 days ago by
Luca
• 0
0
votes
0
replies
24
views
News:
Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano
GSEABase
pheatmap
Workshop
DESeq2
1 day ago
Frances Turner
▴ 20
0
votes
0
replies
30
views
How to convert .raw data for use in xcms
xcms
1 day ago
Monica
• 0
0
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0
replies
28
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Job:
Open Positions for Doctoral Researchers in Molecular Medicine
JobPosting
1 day ago
rubina.tabassum
• 0
1
vote
2
replies
88
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Incosistencies in buildSNNGraph() function
scran
seurat
updated 2 days ago by
ATpoint
★ 5.0k • written 2 days ago by
Lucas
• 0
1
vote
0
replies
56
views
News:
Bioconductor Maintainer Application
maintainer
policy
Bioconductor
Devel
devel
4 days ago
shepherl
4.3k
0
votes
1
reply
434
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
written 10 months ago by
info
▴ 10
0
votes
1
reply
309
views
News:
Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
written 6 months ago by
Wei Shi
★ 3.6k
0
votes
2
replies
2.5k
views
ChAMP pipeline error (champ.import)
software error
written 6.8 years ago by
mhebba
• 0
0
votes
1
reply
132
views
Combining two proteomics datasets with limpa
limpa
ProteomicsWorkflow
limma
updated 5 days ago by
Gordon Smyth
53k • written 5 days ago by
Andrew Pattison
• 0
0
votes
0
replies
87
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Job:
Jobs at Ensembl
ensembldb
7 days ago
Aleena_Ensembl
▴ 30
0
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0
replies
11
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Spam:
Is there a way to map Excel fields to VCF contacts for accurate conversion?
ComputationalChemistry
Technology
Software
Website
updated 7 days ago by
shepherl
4.3k • written 7 days ago by
witebir963
0
0
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0
replies
59
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Job:
Job:Computational Biologist position at the University of Alabama at Birmingham
hiring
RNASeq
JobPosting
SingleCell
SpatialData
8 days ago
lianov
• 0
2
votes
3
replies
169
views
please provide a BibTeX citation for "Advanced Single-Cell Analysis with Bioconductor"
Bioconductor
written 8 days ago by
Victor
▴ 10
2
votes
4
replies
191
views
Converting Probe IDs to HGNC symbols
Annotation
biomaRt
GEOquery
written 10 days ago by
Manav
▴ 10
0
votes
3
replies
235
views
How to do differential expresion across time serise with edgeR?
edgeR
timecoursedata
updated 9 days ago by
Gordon Smyth
53k • written 11 days ago by
petergrahamclark
▴ 10
2
votes
3
replies
379
views
Guitar R package requires update due to dependency GenomicFeatures
GenomicFeatures
Guitar
txdbmaker
GenomicRanges
written 15 days ago by
ferran.llobet.cabau
▴ 10
0
votes
2
replies
157
views
ATACseq rudimentary questions
ATACSeq
DiffBind
17 days ago • updated 10 days ago
4747
• 0
1
vote
1
reply
177
views
How to install packages such as TCGAbiolinks, SumarizedExperiment?
TCGAbiolinks
SummarizedExperiment
updated 12 days ago by
Gordon Smyth
53k • written 13 days ago by
NewRUser
• 0
0
votes
4
replies
5.5k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 2.8 years ago by
mauricio.microbiol
• 0
4
votes
2
replies
315
views
Limma-voom sample weights and impact on DEG numbers
limma
21 days ago • updated 8 days ago
A.Barden
▴ 20
0
votes
1
reply
218
views
wgcna module preseravtion taking too long?
WGCNA
updated 21 days ago by
ATpoint
★ 5.0k • written 28 days ago by
lamia11me
• 0
0
votes
1
reply
302
views
Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCPlus)
HiC
HiCDCPlus
written 5 weeks ago by
Chaoability
• 0
0
votes
3
replies
238
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
written 24 days ago by
ja569116
• 0
0
votes
6
replies
2.8k
views
Ensembl site unresponsive via biomaRt
biomaRt
written 9 months ago by
hebda
• 0
0
votes
3
replies
266
views
segfault in edgeR glmQLFit
edgeR
updated 21 days ago by
Gordon Smyth
53k • written 25 days ago by
Mark
• 0
0
votes
4
replies
568
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 8 days ago by
jtsy6383
• 0 • written 26 days ago by
Durian
• 0
0
votes
1
reply
217
views
News:
Opportunity to host EuroBioC2026 Preconference workshops!
Conference
Workshop
Bioconductor
written 27 days ago by
laurah ondari
• 0
0
votes
1
reply
148
views
NUPOP usage
TOAST
updated 4 weeks ago by
shepherl
4.3k • written 4 weeks ago by
Mohammad
• 0
1
vote
2
replies
335
views
News:
Important: Bioconductor Release 3.22 Delayed
release
written 11 weeks ago by
shepherl
4.3k
0
votes
2
replies
281
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 5 weeks ago by
Michael Love
43k • written 5 weeks ago by
Benjamin
• 0
0
votes
1
reply
214
views
PTM analysis in LIMPA
limpa
updated 5 weeks ago by
Gordon Smyth
53k • written 5 weeks ago by
Diego FGR
• 0
1
vote
1
reply
258
views
News:
Upcoming Ensembl API and data access changes - new blog post available
ensembl
mart
biomaRt
ensembldb
written 6 weeks ago by
Ensembl_Jorge
▴ 10
0
votes
2
replies
259
views
problem reading bam files into nucleR
nucleR
updated 6 weeks ago by
James W. MacDonald
68k • written 6 weeks ago by
efoss
▴ 10
0
votes
0
replies
14
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
6 weeks ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
TOAST
6 weeks ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
6 weeks ago
Maya
0
0
votes
0
replies
8
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
6 weeks ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
6 weeks ago
Maya
0
3
votes
6
replies
1.0k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 7 weeks ago by
Ahmed Salah
• 0
0
votes
1
reply
1.3k
views
two questions about limma
Microarray
limma
Microarray
limma
updated 6 weeks ago by
Gordon Smyth
53k • written 18.9 years ago by
De-Jian ZHAO
▴ 240
0
votes
1
reply
212
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 6 weeks ago by
ATpoint
★ 5.0k • written 6 weeks ago by
Junmo
• 0
0
votes
1
reply
296
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
written 6 weeks ago by
laurah ondari
• 0
0
votes
1
reply
172
views
PFAM formats changed - is it still possible to use this with ISA?
IsoformSwitchAnalyzeR
written 6 weeks ago by
bolusharris
• 0
0
votes
3
replies
299
views
DECIPHER DesignProbes unable to design FISH-probes
decipher
FISH
DECIPHER
FISH-probe
probe-design
written 7 weeks ago by
vreinmuth
• 0
0
votes
2
replies
1.3k
views
p.adjust BH Question
written 14.3 years ago by
David Young
▴ 10
46,718 results • Page
1 of 935
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Replies
Comment: Clarification on counting in Rsubread (featureCounts)
by
Gordon Smyth
53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package
by
Nguyen
• 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
James W. MacDonald
68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
jason.chai
• 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts)
by
Luca
• 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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