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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 29 days ago
shepherl
3.9k
0
votes
7
replies
742
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 23 days ago
shepherl
3.9k
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
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 2 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
7
votes
38
replies
5.7k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 2 hours ago by
Johannes Rainer
★ 2.0k • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
2
votes
4
replies
276
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
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
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
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 49 minutes ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 16 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
0
votes
2
replies
157
views
DESeq2 v1.35.0
DESeq2
updated 14 days ago by
Michael Love
42k • written 14 days ago by
Espresso
• 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
3
votes
4
replies
265
views
Store output of matchPWM()
biostrings
Biostrings
15 days ago • updated 3 days ago
mat149
▴ 70
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
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
4
votes
9
replies
488
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 9 days ago
Juan Higareda
• 0
0
votes
4
replies
291
views
DEG with low counts
DESeq2
updated 27 days ago by
Michael Love
42k • written 4 weeks ago by
Rajat
• 0
0
votes
6
replies
282
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 13 days ago by
swbarnes2
★ 1.4k • written 14 days ago by
arfranco
▴ 130
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
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
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
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
0
votes
3
replies
8.4k
views
SingleR Label.Ont
SingleR
updated 5 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
2
replies
109
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 2 days ago by
zhouwanding
▴ 10 • written 4 days ago by
Seungmin
• 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
0
votes
3
replies
173
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
bas_work
▴ 30
1
vote
2
replies
395
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
Kim
• 0
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 11 days ago
Henrik Bengtsson
★ 2.4k
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 24 days ago by
James W. MacDonald
65k • written 27 days ago by
John
• 0
1
vote
3
replies
234
views
Different Shrunk Log2FC according with reference
DESeq2
updated 22 days ago by
Michael Love
42k • written 23 days ago by
andrebolerbarros
▴ 20
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
0
votes
4
replies
358
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by
Ziliang
• 0 • written 15 days ago by
Ian D.
▴ 70
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
1
vote
2
replies
107
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
2 days ago • updated 1 day ago
Daniel
• 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
1
vote
4
replies
225
views
minfi::read.metharray.exp
minfiData
minfi
updated 23 days ago by
Basti
▴ 780 • written 24 days ago by
clacarion
• 0
1
vote
1
reply
151
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 days ago by
Leo Lahti
▴ 40 • written 20 days ago by
Dario Strbenac
★ 1.5k
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
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
1
vote
2
replies
173
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
22 days ago
ATpoint
★ 4.1k
1
vote
7
replies
355
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
21 days ago • updated 20 days ago
pl23
• 0
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
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 22 days ago by
Michael Love
42k • written 22 days ago by
kcarey
• 0
1
vote
2
replies
74
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
2 days ago • updated 1 day ago
Patadù
▴ 10
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
0
votes
3
replies
208
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 27 days ago by
Gordon Smyth
50k • written 28 days ago by
prity6459
• 0
0
votes
1
reply
96
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 7 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
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
1
vote
2
replies
262
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 27 days ago
Weiqian
▴ 10
0
votes
3
replies
271
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 16 days ago by
James W. MacDonald
65k • written 17 days ago by
SSSJec
• 0
194 results • Page
1 of 4
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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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