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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 7 days ago
shepherl
3.8k
0
votes
7
replies
612
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 2 days ago
shepherl
3.8k
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 23 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
2
votes
8
replies
490
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 28 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Amit
• 0
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 21 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
4
votes
8
replies
341
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 6 days ago by
Peter Hickey
▴ 740 • written 14 days ago by
Juan Higareda
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 7 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 11 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
1
vote
10
replies
405
views
Obtaining pheno data from CEL files
GEO
affy
23 days ago • updated 16 days ago
Kurtis
• 0
0
votes
2
replies
213
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
28 days ago • updated 23 days ago
w.cookson
• 0
1
vote
3
replies
321
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 10 days ago by
Gordon Smyth
50k • written 15 days ago by
Simran
• 0
6
votes
16
replies
2.3k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 21 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 22 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
2
votes
2
replies
139
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
sansan
• 0
0
votes
6
replies
307
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 14 days ago by
Tim Peters
▴ 170 • written 23 days ago by
s.malik
• 0
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 3 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
6
replies
313
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 27 days ago by
Faisal
• 0
0
votes
3
replies
102
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
bas_work
▴ 30
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 19 days ago by
Michael
▴ 10 • written 24 months ago by
axe880
• 0
0
votes
18
replies
2.4k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
0
votes
2
replies
1.0k
views
error when using M-values in ChAMP
ChAMP
updated 28 days ago by
hortense96
• 0 • written 6.3 years ago by
a.mcneill
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 3 days ago
shepherl
3.8k
1
vote
6
replies
456
views
GSVA on separate healthy and disease datasets
GSVA
updated 15 days ago by
James W. MacDonald
65k • written 16 days ago by
Lucy
▴ 60
0
votes
4
replies
199
views
Storing directories inside an ExperimentHub package?
ExperimentHub
14 days ago • updated 13 days ago
Tim Barry
• 0
1
vote
4
replies
144
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 3 days ago by
James W. MacDonald
65k • written 6 days ago by
Mirella Aurora
• 0
0
votes
4
replies
154
views
flowStats Search Error
flowStats
updated 8 days ago by
shepherl
3.8k • written 9 days ago by
tholmes
• 0
3
votes
3
replies
287
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 17 days ago by
Netanel
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 6 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
12
votes
12
replies
764
views
Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by
Robert Castelo
★ 3.3k • written 5 days ago by
Chris
• 0
0
votes
1
reply
214
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 21 days ago by
Tim Peters
▴ 170 • written 21 days ago by
Kim
• 0
1
vote
3
replies
90
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
1
vote
2
replies
212
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
4 weeks ago • updated 29 days ago
Chanderkant Chaudhary
• 0
2
votes
5
replies
126
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 1 hour ago by
James W. MacDonald
65k • written 1 day ago by
bandconductor
• 0
0
votes
2
replies
898
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
2
replies
166
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
24 days ago • updated 23 days ago
Seongsu
• 0
0
votes
1
reply
120
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 15 days ago by
ATpoint
★ 4.0k • written 17 days ago by
Merav
• 0
1
vote
1
reply
72
views
Citation for edgeR user guide
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
k___
▴ 30
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
23 days ago • updated 22 days ago
michelafrancesconi8
• 0
0
votes
1
reply
142
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by
Michael Love
41k • written 27 days ago by
Mikushi
• 0
0
votes
5
replies
211
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 1 day ago by
James W. MacDonald
65k • written 3 days ago by
Gayatri
• 0
2
votes
5
replies
141
views
get BM error
ensembldb
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
Fara
• 0
0
votes
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 7 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
1
reply
126
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Reeya
• 0
0
votes
2
replies
325
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
4 weeks ago • updated 22 days ago
Gordon
• 0
2
votes
5
replies
1000
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 20 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
1
vote
2
replies
164
views
Design Matrix within group comparison more than two groups
DESeq2
13 days ago • updated 12 days ago
hemantcnaik
• 0
203 results • Page
1 of 5
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
SamGG
▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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