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Chip Seq Analysis of RNA Polymerase 2
ChIPseeker
ChIPSeqData
ChIPSeq
Bioconductor
18 hours ago
Gaurav
• 0
4
votes
3
replies
506
views
Limma-voom sample weights and impact on DEG numbers
limma
written 6 weeks ago by
A.Barden
▴ 20
0
votes
0
replies
28
views
Job:
Postdoctoral Fellow (Computational Biology / Bioinformatics) - Neuroepigenetics (MSCA PF / EMBO)
Epigenetics
JobPosting
Neuroscience
1 day ago
lalit.kaurani
• 0
0
votes
0
replies
46
views
News:
The Call for Abstracts for BioC2026 is open!
Bioconductor
Conference
1 day ago
laurah ondari
• 0
0
votes
3
replies
250
views
Confirm that OpenStats will not be archived (pryr dependency)
OpenStats
written 8 days ago by
Marina
• 0
0
votes
15
replies
1.4k
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics
dada2
MicrobiomeData
written 19 months ago by
abhisek001
• 0
20
votes
6
replies
11k
views
Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
written 7.0 years ago by
shepherl
4.3k
0
votes
0
replies
14
views
Spam:
PokeChill
customCMPdb
AMOUNTAIN
3 days ago
play
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
1
reply
109
views
msmsTests, inconsistent sign between lFC.Av and LogFC
msmsTests
Proteomics
5 days ago
Ben
• 0
0
votes
1
reply
111
views
DESeq2 for 16S rRNA Analysis
DESeq2
updated 5 days ago by
James W. MacDonald
68k • written 6 days ago by
lizflor
• 0
0
votes
0
replies
58
views
News:
Deadline Extended: EuroBioC2026 Call for Abstracts
Bioconductor
Conference
5 days ago
laurah ondari
• 0
0
votes
3
replies
1.5k
views
ChAMP trouble reading csv file
ChAMP
written 2.5 years ago by
Keasiykan
• 0
0
votes
0
replies
51
views
bcftools norm Equivalent
Rsamtools
8 days ago
Dario Strbenac
★ 1.6k
0
votes
5
replies
234
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq
DESeq2
DifferentialExpression
updated 8 days ago by
Michael Love
43k • written 8 days ago by
Ahmed Salah
• 0
0
votes
2
replies
183
views
lfc shrinkage estimator in DESeq2
DESeq2
written 9 days ago by
julia_mcdonough
• 0
2
votes
1
reply
172
views
Array weights in dpcDE
limpa
updated 9 days ago by
Gordon Smyth
53k • written 9 days ago by
Matt
• 0
0
votes
2
replies
143
views
Justify title track when rotation = 0
Gviz
gviz
written 14 days ago by
Xenia
• 0
0
votes
2
replies
175
views
Bile acid analysis with limpa
limpa
MassSpectrometry
MassSpectrometryData
updated 10 days ago by
Gordon Smyth
53k • written 14 days ago by
DN
• 0
0
votes
13
replies
796
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 9 days ago by
Gordon Smyth
53k • written 15 days ago by
chp265
• 0
0
votes
1
reply
118
views
Changing multiple display parameters of a specific exon in GeneRegionTrack
Gviz
written 14 days ago by
Xenia
• 0
0
votes
2
replies
275
views
Are individual-mouse-based statistics possible in CellChat?
Bioconductor
CellChat
updated 11 days ago by
LillianaVolkman99
• 0 • written 21 days ago by
Omer
• 0
0
votes
6
replies
609
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 16 days ago by
Martin Morgan
25k • written 8 weeks ago by
Benjamin
• 0
0
votes
1
reply
258
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage
DESeq2
contrast
updated 15 days ago by
ATpoint
★ 5.0k • written 19 days ago by
ja569116
• 0
2
votes
6
replies
468
views
limpa analysis advice
limpa
updated 7 days ago by
Gordon Smyth
53k • written 19 days ago by
SamGG
▴ 360
0
votes
1
reply
129
views
News:
The BioC2026 Sticker Design Contest is Open!
Bioconductor
Conference
written 19 days ago by
laurah ondari
• 0
4
votes
2
replies
335
views
When to use edgeR or limma
edgeR
limma
updated 19 days ago by
Gordon Smyth
53k • written 21 days ago by
abzhang97
• 0
1
vote
3
replies
222
views
Incosistencies in buildSNNGraph() function
scran
seurat
written 25 days ago by
Lucas
• 0
0
votes
2
replies
977
views
A problem occurs when running the monocle2
monocle
written 4 months ago by
yuheng_yang
• 0
0
votes
7
replies
523
views
limpa-blank normalization and Spectronaut's PTM stoichiometry
limpa
updated 14 days ago by
Gordon Smyth
53k • written 21 days ago by
emily.wolfrum
• 0
0
votes
2
replies
139
views
Questions about bacon QC and correction on EWAS results
bacon
updated 19 hours ago by
Tikaaa2sahaaaq2c
• 0 • written 21 days ago by
sup0903
• 0
3
votes
4
replies
313
views
Question about the filterByExpr function inputs in edgeR
RNASeq
filter
design
edgeR
model.matrix
22 days ago • updated 21 days ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
138
views
Development of MSstat workflow to analyze DIA time series data
MSstats
updated 22 days ago by
Gordon Smyth
53k • written 22 days ago by
sithurandi
• 0
0
votes
0
replies
263
views
MSstatsPTM-SpectronauttoMSstatsPTMFormat-failing with TAIR10 Locus Tags: Issue with UniProt-centric protein ID parsing
Bioconductor
MSstatsPTM
22 days ago
srkingwu
• 0
8
votes
8
replies
2.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq
edger
differential gene expression
batch effect
written 7.4 years ago by
Laura
▴ 20
0
votes
0
replies
93
views
Junction CPM via Snapcount and Recount3
snapcount
recount3
23 days ago
henry.tietz
• 0
3
votes
4
replies
439
views
Clarification on counting in Rsubread (featureCounts)
featureCounts
Rsubread
updated 22 days ago by
Gordon Smyth
53k • written 7 weeks ago by
Luca
• 0
0
votes
1
reply
121
views
News:
Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano
GSEABase
pheatmap
Workshop
DESeq2
written 23 days ago by
Frances Turner
▴ 20
0
votes
1
reply
126
views
How to convert .raw data for use in xcms
xcms
written 23 days ago by
Monica
• 0
0
votes
1
reply
323
views
Job:
Open Positions for Doctoral Researchers in Molecular Medicine
JobPosting
written 23 days ago by
rubina.tabassum
• 0
1
vote
1
reply
173
views
News:
Bioconductor Maintainer Application
maintainer
policy
Bioconductor
Devel
devel
written 26 days ago by
shepherl
4.3k
0
votes
1
reply
489
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
written 11 months ago by
info
▴ 10
0
votes
1
reply
369
views
News:
Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
written 7 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
2
replies
331
views
Combining two proteomics datasets with limpa
limpa
ProteomicsWorkflow
limma
28 days ago • updated 14 days ago
Andrew Pattison
• 0
0
votes
0
replies
167
views
Job:
Jobs at Ensembl
ensembldb
29 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 29 days ago by
shepherl
4.3k • written 29 days ago by
witebir963
0
0
votes
0
replies
113
views
Job:
Job:Computational Biologist position at the University of Alabama at Birmingham
hiring
RNASeq
JobPosting
SingleCell
SpatialData
4 weeks ago
lianov
• 0
2
votes
3
replies
249
views
please provide a BibTeX citation for "Advanced Single-Cell Analysis with Bioconductor"
Bioconductor
written 4 weeks ago by
Victor
▴ 10
2
votes
4
replies
272
views
Converting Probe IDs to HGNC symbols
Annotation
biomaRt
GEOquery
written 4 weeks ago by
Manav
▴ 10
46,742 results • Page
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Comment: using limma trend workflow in CAMERA
by
Gordon Smyth
53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results
by
Tikaaa2sahaaaq2c
• 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA
by
A.Barden
▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Tikaaa2sahaaaq2c
• 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase
by
DamionLedner99
• 0
thanks for sharing!!! https://cran.r-project.org/
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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fl
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James W. MacDonald
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