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Bulk RNAseq analysis for
DESeq2
RNASeq
edgeR
limma
updated 8 hours ago by
Gordon Smyth
53k • written 13 hours ago by
Mariami
• 0
0
votes
0
replies
16
views
Spam:
What are the various factors which make affordable 2 BHK flats in Gurgaon the best option for first-time buyers?
mouse430a2.db
16 hours ago
reeltor537
0
0
votes
5
replies
2.3k
views
DESeq2 contrast cleaning problem
software error
bugs
deseq2
written 10.0 years ago by
john.hu
• 0
0
votes
3
replies
2.4k
views
PCA outliers cleaning
scRNAseq
Pipeline
Seurat
SingleCellExperiment
written 6.3 years ago by
albadrs.93
▴ 10
1
vote
2
replies
2.8k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
written 3.9 years ago by
forlani.luca
• 0
0
votes
2
replies
125
views
soGGi error
soGGi
written 4 days ago by
Daniel
• 0
0
votes
1
reply
114
views
Chip Seq Analysis of RNA Polymerase 2
ChIPseeker
ChIPSeqData
ChIPSeq
Bioconductor
written 5 days ago by
Gaurav
• 0
5
votes
3
replies
589
views
Limma-voom sample weights and impact on DEG numbers
limma
written 6 weeks ago by
A.Barden
▴ 20
0
votes
1
reply
167
views
Job:
Postdoctoral Fellow (Computational Biology / Bioinformatics) - Neuroepigenetics (MSCA PF / EMBO)
Epigenetics
JobPosting
Neuroscience
updated 2 days ago by
mudasarnaeem2020
• 0 • written 6 days ago by
lalit.kaurani
• 0
0
votes
1
reply
161
views
News:
The Call for Abstracts for BioC2026 is open!
Bioconductor
Conference
written 6 days ago by
laurah ondari
• 0
0
votes
3
replies
284
views
Confirm that OpenStats will not be archived (pryr dependency)
OpenStats
written 13 days ago by
Marina
• 0
0
votes
15
replies
1.5k
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
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Spam:
PokeChill
customCMPdb
AMOUNTAIN
7 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
131
views
msmsTests, inconsistent sign between lFC.Av and LogFC
msmsTests
Proteomics
10 days ago
Ben
• 0
0
votes
1
reply
134
views
DESeq2 for 16S rRNA Analysis
DESeq2
updated 10 days ago by
James W. MacDonald
68k • written 11 days ago by
lizflor
• 0
0
votes
0
replies
104
views
News:
Deadline Extended: EuroBioC2026 Call for Abstracts
Bioconductor
Conference
10 days ago
laurah ondari
• 0
0
votes
3
replies
1.5k
views
ChAMP trouble reading csv file
ChAMP
written 2.6 years ago by
Keasiykan
• 0
0
votes
0
replies
59
views
bcftools norm Equivalent
Rsamtools
13 days ago
Dario Strbenac
★ 1.6k
0
votes
5
replies
252
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq
DESeq2
DifferentialExpression
updated 13 days ago by
Michael Love
43k • written 13 days ago by
Ahmed Salah
• 0
0
votes
2
replies
200
views
lfc shrinkage estimator in DESeq2
DESeq2
written 14 days ago by
julia_mcdonough
• 0
2
votes
1
reply
191
views
Array weights in dpcDE
limpa
updated 13 days ago by
Gordon Smyth
53k • written 14 days ago by
Matt
• 0
0
votes
2
replies
162
views
Justify title track when rotation = 0
Gviz
gviz
written 19 days ago by
Xenia
• 0
0
votes
2
replies
183
views
Bile acid analysis with limpa
limpa
MassSpectrometry
MassSpectrometryData
updated 15 days ago by
Gordon Smyth
53k • written 18 days ago by
DN
• 0
0
votes
13
replies
834
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 14 days ago by
Gordon Smyth
53k • written 20 days ago by
chp265
• 0
0
votes
1
reply
165
views
Changing multiple display parameters of a specific exon in GeneRegionTrack
Gviz
written 19 days ago by
Xenia
• 0
0
votes
2
replies
305
views
Are individual-mouse-based statistics possible in CellChat?
Bioconductor
CellChat
updated 16 days ago by
LillianaVolkman99
• 0 • written 26 days ago by
Omer
• 0
0
votes
6
replies
627
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 21 days ago by
Martin Morgan
25k • written 9 weeks ago by
Benjamin
• 0
0
votes
1
reply
275
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage
DESeq2
contrast
updated 20 days ago by
ATpoint
★ 5.0k • written 24 days ago by
ja569116
• 0
2
votes
6
replies
502
views
limpa analysis advice
limpa
updated 12 days ago by
Gordon Smyth
53k • written 24 days ago by
SamGG
▴ 360
0
votes
1
reply
146
views
News:
The BioC2026 Sticker Design Contest is Open!
Bioconductor
Conference
written 24 days ago by
laurah ondari
• 0
4
votes
2
replies
364
views
When to use edgeR or limma
edgeR
limma
updated 24 days ago by
Gordon Smyth
53k • written 26 days ago by
abzhang97
• 0
1
vote
3
replies
242
views
Incosistencies in buildSNNGraph() function
scran
seurat
written 4 weeks ago by
Lucas
• 0
0
votes
2
replies
1.1k
views
A problem occurs when running the monocle2
monocle
written 4 months ago by
yuheng_yang
• 0
0
votes
7
replies
570
views
limpa-blank normalization and Spectronaut's PTM stoichiometry
limpa
updated 19 days ago by
Gordon Smyth
53k • written 26 days ago by
emily.wolfrum
• 0
0
votes
2
replies
188
views
Questions about bacon QC and correction on EWAS results
bacon
written 26 days ago by
sup0903
• 0
3
votes
4
replies
362
views
Question about the filterByExpr function inputs in edgeR
RNASeq
filter
design
edgeR
model.matrix
27 days ago • updated 26 days ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
156
views
Development of MSstat workflow to analyze DIA time series data
MSstats
updated 27 days ago by
Gordon Smyth
53k • written 27 days ago by
sithurandi
• 0
0
votes
0
replies
330
views
MSstatsPTM-SpectronauttoMSstatsPTMFormat-failing with TAIR10 Locus Tags: Issue with UniProt-centric protein ID parsing
Bioconductor
MSstatsPTM
27 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
1
reply
134
views
Junction CPM via Snapcount and Recount3
snapcount
recount3
written 28 days ago by
henry.tietz
• 0
3
votes
4
replies
474
views
Clarification on counting in Rsubread (featureCounts)
featureCounts
Rsubread
updated 27 days ago by
Gordon Smyth
53k • written 8 weeks ago by
Luca
• 0
0
votes
1
reply
142
views
News:
Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano
GSEABase
pheatmap
Workshop
DESeq2
written 28 days ago by
Frances Turner
▴ 20
0
votes
1
reply
158
views
How to convert .raw data for use in xcms
xcms
written 28 days ago by
Monica
• 0
0
votes
1
reply
358
views
Job:
Open Positions for Doctoral Researchers in Molecular Medicine
JobPosting
written 28 days ago by
rubina.tabassum
• 0
1
vote
1
reply
183
views
News:
Bioconductor Maintainer Application
maintainer
policy
Bioconductor
Devel
devel
written 4 weeks ago by
shepherl
4.3k
0
votes
1
reply
501
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
written 11 months ago by
info
▴ 10
0
votes
1
reply
404
views
News:
Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
updated 8 hours ago by
a2a2haa
• 0 • 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
46,745 results • Page
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Answer: Bulk RNAseq analysis for
by
Gordon Smyth
53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Comment: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open fo
by
a2a2haa
• 0
By promoting reproducible analysis, the scientific community can better understand the precise mechanisms that make [Hydrogen inhalation sa…
Answer: Bulk RNAseq analysis for
by
James W. MacDonald
68k
In my experience, the within-clone variability of differentiated stem cells is often as large or larger than the between-clone variability,…
Comment: Jobs at Ensembl
by
frostybuddyy
• 0
I found your blog "Jobs at Ensembl" quite fascinating! The way you talked about the convergence of bioinformatics and data science in emplo…
Comment: Postdoctoral Fellow (Computational Biology / Bioinformatics) - Neuroepigenetics
by
mudasarnaeem2020
• 0
Promoting UDISE+ Features on Social Media to Increase Awareness https://udisseplus.com/[enter link description here][1] [1]: https://ud…
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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