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Votes
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
37
replies
5.7k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 7 hours ago by
Daniele
• 0 • 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
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
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
19
replies
2.5k
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
3
replies
304
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 6 days ago by
Gordon Smyth
50k • written 28 days ago by
Shaimaa Gamal
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 23 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
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
5
votes
9
replies
972
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
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
4
votes
2
replies
617
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
0
replies
131
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
15 days ago
shepherl
3.9k
4
votes
9
replies
487
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 9 days ago
Juan Higareda
• 0
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
310
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
212
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 16 hours ago by
ATpoint
★ 4.1k • written 1 day ago by
pangtaihin
• 0
4
votes
6
replies
463
views
FilterByExpr low counts with small sample size
edgeR
29 days ago • updated 24 days ago
Jonathan
▴ 10
3
votes
5
replies
282
views
Help with running egsea()
EGSEA
10 days ago • updated 9 days ago
Chris
▴ 10
3
votes
3
replies
242
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
4 weeks ago • updated 28 days ago
jacques.imbert
• 0
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
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
3
replies
365
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
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
4
replies
264
views
Store output of matchPWM()
biostrings
Biostrings
15 days ago • updated 3 days ago
mat149
▴ 70
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
1
reply
142
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
501
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
3
replies
264
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
bioinf
▴ 10
3
votes
10
replies
433
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
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
4
replies
259
views
Help with error using camera() in limma
CAMERA
limma
16 days ago
Chris
▴ 10
2
votes
1
reply
55
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 3 days ago by
Sara
• 0
2
votes
7
replies
353
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
8 days ago • updated 5 days ago
sajadahmad41454
• 0
2
votes
1
reply
155
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
e1271094
• 0
2
votes
1
reply
140
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 10 days ago by
Michael Love
42k • written 10 days ago by
mat149
▴ 70
2
votes
9
replies
423
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
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
2
replies
263
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
9 days ago • updated 3 days ago
zzrammal
• 0
2
votes
5
replies
788
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
4
replies
274
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
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
3
replies
73
views
Problem installing ChAMP on a MacBook
ChAMP
updated 17 hours ago by
shepherl
3.9k • written 1 day ago by
Galia
• 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
3
replies
101
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
194 results • Page
1 of 4
Recent ...
Replies
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…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
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
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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