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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 17 days ago
shepherl
3.9k
0
votes
7
replies
695
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 11 days ago
shepherl
3.9k
0
votes
26
replies
2.4k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
15 months ago • updated 9 hours ago
Poonam
• 0
3
votes
3
replies
332
views
permutation test in edgeR
rna-seq
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 26 days ago by
Netanel
• 0
1
vote
4
replies
234
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 12 days ago by
James W. MacDonald
65k • written 16 days ago by
Mirella Aurora
• 0
0
votes
6
replies
172
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 1 day ago by
swbarnes2
★ 1.3k • written 2 days ago by
arfranco
▴ 130
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by
mauricio.microbiol
• 0
0
votes
4
replies
263
views
DEG with low counts
DESeq2
updated 15 days ago by
Michael Love
41k • written 20 days ago by
Rajat
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
14 days ago • updated 3 days ago
Chris
• 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
6
replies
334
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 24 days ago by
Tim Peters
▴ 180 • written 4 weeks ago by
s.malik
• 0
1
vote
2
replies
308
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
Kim
• 0
1
vote
3
replies
347
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
1
vote
10
replies
452
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 25 days ago
Kurtis
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 16 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 4 days ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
1
vote
6
replies
490
views
GSVA on separate healthy and disease datasets
GSVA
updated 24 days ago by
James W. MacDonald
65k • written 25 days ago by
Lucy
▴ 60
4
votes
8
replies
391
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 16 days ago by
Peter Hickey
▴ 740 • written 23 days ago by
Juan Higareda
• 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 4 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 13 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 16 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
2
votes
2
replies
187
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 15 days ago by
James W. MacDonald
65k • written 16 days ago by
sansan
• 0
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 12 days ago
shepherl
3.9k
0
votes
4
replies
222
views
Storing directories inside an ExperimentHub package?
ExperimentHub
24 days ago • updated 23 days ago
Tim Barry
• 0
0
votes
4
replies
193
views
flowStats Search Error
flowStats
updated 18 days ago by
shepherl
3.9k • written 19 days ago by
tholmes
• 0
0
votes
3
replies
151
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
bas_work
▴ 30
0
votes
2
replies
82
views
DESeq2 v1.35.0
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Espresso
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 4 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 21 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 29 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
1
vote
2
replies
240
views
How to retrieve detailed regression results from deseq2
DESeq2
24 days ago • updated 15 days ago
Weiqian
▴ 10
0
votes
2
replies
113
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
4 days ago • updated 1 day ago
Aurora
• 0
0
votes
1
reply
133
views
covariate with negative and positive values
DESeq2
updated 16 days ago by
Michael Love
41k • written 18 days ago by
Brynn
• 0
0
votes
2
replies
201
views
PCA plot suggestions
DESeq2
PCAtools
updated 8 days ago by
Michael Love
41k • written 10 days ago by
Aaliya
• 0
0
votes
1
reply
130
views
ATACseq merge peaks
DiffBind
updated 8 days ago by
ATpoint
★ 4.1k • written 10 days ago by
Shloka
• 0
3
votes
3
replies
218
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 5 days ago by
ATpoint
★ 4.1k • written 6 days ago by
bioinf
▴ 10
0
votes
2
replies
118
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 2 days ago
Ian D.
▴ 70
0
votes
1
reply
153
views
Adding columns to DEXSeqResults object
DEXSeq
updated 16 days ago by
Alejandro Reyes
★ 1.9k • written 18 days ago by
Clyde
• 0
1
vote
1
reply
166
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 8 days ago by
Gordon Smyth
50k • written 12 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
4
replies
203
views
minfi::read.metharray.exp
minfiData
minfi
updated 10 days ago by
Basti
▴ 780 • written 12 days ago by
clacarion
• 0
0
votes
2
replies
791
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
1
vote
2
replies
707
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
17 days ago • updated 8 days ago
ussarizona
▴ 10
0
votes
1
reply
149
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 10 days ago by
Michael Love
41k • written 10 days ago by
kcarey
• 0
0
votes
3
replies
229
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 4 days ago by
James W. MacDonald
65k • written 5 days ago by
SSSJec
• 0
1
vote
7
replies
311
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
9 days ago • updated 8 days ago
pl23
• 0
0
votes
4
replies
199
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
16 days ago
sropri
• 0
1
vote
2
replies
511
views
GSVA error
GSVA
20 days ago • updated 19 days ago
Alex
• 0
0
votes
5
replies
296
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 10 days ago by
James W. MacDonald
65k • written 13 days ago by
Gayatri
• 0
0
votes
4
replies
307
views
Help with design.matrix
limma
29 days ago • updated 28 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
161
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 25 days ago by
Michael Love
41k • written 25 days ago by
Adelaide
• 0
198 results • Page
1 of 4
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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