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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 16 days ago
shepherl
3.9k
0
votes
7
replies
692
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 10 days ago
shepherl
3.9k
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 29 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 28 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
1
vote
4
replies
225
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 11 days ago by
James W. MacDonald
65k • written 15 days ago by
Mirella Aurora
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
4
replies
261
views
DEG with low counts
DESeq2
updated 14 days ago by
Michael Love
41k • written 19 days ago by
Rajat
• 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
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 3 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
13 days ago • updated 2 days ago
Chris
• 0
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 11 days ago
shepherl
3.9k
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 15 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 20 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
1
vote
3
replies
345
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 19 days ago by
Gordon Smyth
50k • written 24 days ago by
Simran
• 0
0
votes
6
replies
332
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 23 days ago by
Tim Peters
▴ 180 • written 4 weeks ago by
s.malik
• 0
0
votes
2
replies
73
views
DESeq2 v1.35.0
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Espresso
• 0
4
votes
8
replies
389
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 15 days ago by
Peter Hickey
▴ 740 • written 22 days ago by
Juan Higareda
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 15 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
1
vote
2
replies
233
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 10 hours ago by
Gordon Smyth
50k • written 13 hours ago by
Kim
• 0
0
votes
3
replies
146
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
bas_work
▴ 30
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 12 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
4
replies
220
views
Storing directories inside an ExperimentHub package?
ExperimentHub
23 days ago • updated 22 days ago
Tim Barry
• 0
0
votes
6
replies
146
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 5 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
arfranco
▴ 130
0
votes
4
replies
190
views
flowStats Search Error
flowStats
updated 17 days ago by
shepherl
3.9k • written 18 days ago by
tholmes
• 0
1
vote
10
replies
451
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 25 days ago
Kurtis
• 0
3
votes
3
replies
327
views
permutation test in edgeR
rna-seq
edgeR
updated 13 days ago by
Gordon Smyth
50k • written 26 days ago by
Netanel
• 0
1
vote
6
replies
485
views
GSVA on separate healthy and disease datasets
GSVA
updated 23 days ago by
James W. MacDonald
65k • written 25 days ago by
Lucy
▴ 60
2
votes
2
replies
183
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 14 days ago by
James W. MacDonald
65k • written 15 days ago by
sansan
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 3 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
2
votes
2
replies
188
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 28 days ago by
ATpoint
★ 4.1k • written 29 days ago by
Dario Strbenac
★ 1.5k
1
vote
4
replies
201
views
minfi::read.metharray.exp
minfiData
minfi
updated 10 days ago by
Basti
▴ 780 • written 11 days ago by
clacarion
• 0
0
votes
1
reply
167
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
gene_bioconductor
▴ 10
0
votes
1
reply
151
views
Adding columns to DEXSeqResults object
DEXSeq
updated 15 days ago by
Alejandro Reyes
★ 1.9k • written 17 days ago by
Clyde
• 0
0
votes
7
replies
306
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
17 days ago • updated 11 days ago
hortense96
• 0
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 3 days ago
Chris
• 0
0
votes
4
replies
306
views
Help with design.matrix
limma
28 days ago • updated 27 days ago
andrea.rodriguez-martinez13
• 0
0
votes
2
replies
191
views
PCA plot suggestions
DESeq2
PCAtools
updated 7 days ago by
Michael Love
41k • written 9 days ago by
Aaliya
• 0
0
votes
1
reply
109
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 15 days ago by
Michael Love
41k • written 16 days ago by
09191919
• 0
0
votes
1
reply
42
views
package goseq seems to be not available on the latest version of R
goseq
updated 11 hours ago by
Gordon Smyth
50k • written 15 hours ago by
Patrycja
• 0
1
vote
4
replies
472
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 2 days ago
JKim
• 0
0
votes
2
replies
106
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
2 days ago • updated 1 day ago
kcarey
• 0
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 29 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
3
votes
1
reply
302
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
i.sudbery
▴ 40
0
votes
1
reply
93
views
putting my own expression data in deseq2
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
Dev
• 0
2
votes
5
replies
249
views
get BM error
ensembldb
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
Fara
• 0
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
23 days ago • updated 14 days ago
Weiqian
▴ 10
1
vote
7
replies
305
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
8 days ago • updated 7 days ago
pl23
• 0
0
votes
2
replies
128
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
15 days ago
prity6459
• 0
3
votes
3
replies
219
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 10 days ago by
Michael Love
41k • written 11 days ago by
WardDeb
• 0
202 results • Page
1 of 5
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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