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15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
26 days ago • updated 15 days ago
Chris
▴ 10
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
6 weeks ago • updated 16 days ago
Chris
▴ 10
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 28 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 28 days ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
7
votes
38
replies
5.7k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 3 hours ago by
Johannes Rainer
★ 2.0k • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
6
votes
5
replies
474
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 11 weeks ago by
Kim
• 0
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 24 days ago
shepherl
3.9k
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 27 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 16 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 29 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 24 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
5
votes
3
replies
304
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 29 days ago by
Shaimaa Gamal
• 0
5
votes
9
replies
973
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 28 days ago
Chris
▴ 10
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 14 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
4
votes
2
replies
618
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
14 days ago • updated 10 days ago
gene_bioconductor
▴ 10
4
votes
6
replies
464
views
FilterByExpr low counts with small sample size
edgeR
29 days ago • updated 24 days ago
Jonathan
▴ 10
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 1 day ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
4
votes
5
replies
312
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
11 days ago • updated 1 day ago
Chris
▴ 10
4
votes
9
replies
488
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 9 days ago
Juan Higareda
• 0
4
votes
9
replies
214
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 21 hours ago by
ATpoint
★ 4.1k • written 2 days ago by
pangtaihin
• 0
4
votes
0
replies
134
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
15 days ago
shepherl
3.9k
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
i.sudbery
▴ 40
3
votes
3
replies
249
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
WardDeb
• 0
3
votes
3
replies
244
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
4 weeks ago • updated 29 days ago
jacques.imbert
• 0
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 9 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
3
votes
1
reply
144
views
How to save the DEXSeq results
DEXSeq
updated 10 days ago by
Michael Love
42k • written 10 days ago by
Sara
• 0
3
votes
4
replies
265
views
Store output of matchPWM()
biostrings
Biostrings
15 days ago • updated 3 days ago
mat149
▴ 70
3
votes
3
replies
366
views
permutation test in edgeR
rna-seq
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
3
votes
4
replies
503
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 8 days ago by
Mike Smith
★ 6.5k • written 11 days ago by
robersy
• 0
3
votes
5
replies
283
views
Help with running egsea()
EGSEA
10 days ago • updated 9 days ago
Chris
▴ 10
3
votes
2
replies
229
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 24 days ago by
Guido Hooiveld
★ 4.0k • written 27 days ago by
fernanda.backsouza
▴ 10
3
votes
18
replies
3.0k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 29 days ago
shepherl
3.9k
3
votes
3
replies
265
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
bioinf
▴ 10
3
votes
10
replies
434
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 6 days ago by
James W. MacDonald
65k • written 9 days ago by
Abbey
• 0
3
votes
4
replies
259
views
Help with error using camera() in limma
CAMERA
limma
16 days ago
Chris
▴ 10
2
votes
7
replies
356
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
9 days ago • updated 5 days ago
sajadahmad41454
• 0
2
votes
4
replies
277
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 24 days ago by
James W. MacDonald
65k • written 28 days ago by
Mirella Aurora
• 0
2
votes
2
replies
221
views
fgsea significant result
fgsea
12 days ago • updated 11 days ago
Chris
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 16 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
2
votes
5
replies
789
views
DESeq2 setting significant p-value
DESeq2
updated 27 days ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
2
votes
9
replies
425
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
Alexandre
• 0
2
votes
13
replies
476
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
25 days ago • updated 22 days ago
fernanda.backsouza
▴ 10
2
votes
3
replies
78
views
Problem installing ChAMP on a MacBook
ChAMP
updated 21 hours ago by
shepherl
3.9k • written 1 day ago by
Galia
• 0
2
votes
3
replies
1.7k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 3 days ago by
bandconductor
• 0 • written 3.6 years ago by
ZheFrench
▴ 60
2
votes
5
replies
165
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
1 day ago • updated 1 hour ago
Patadù
▴ 10
2
votes
3
replies
103
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
Guillermo
• 0
2
votes
2
replies
209
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
sansan
• 0
2
votes
2
replies
231
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
17 days ago
Chris
▴ 10
194 results • Page
1 of 4
Recent ...
Replies
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning
by
angelaesper43
• 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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