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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 15 days ago
shepherl
3.9k
0
votes
7
replies
687
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 9 days ago
shepherl
3.9k
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 28 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 2 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
4
replies
183
views
flowStats Search Error
flowStats
updated 16 days ago by
shepherl
3.9k • written 17 days ago by
tholmes
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 14 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
2
replies
50
views
DESeq2 v1.35.0
DESeq2
updated 12 hours ago by
Michael Love
41k • written 13 hours ago by
Espresso
• 0
0
votes
3
replies
145
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
bas_work
▴ 30
6
votes
19
replies
2.4k
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
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 11 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
22 days ago • updated 21 days ago
Tim Barry
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 14 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
6
replies
330
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 22 days ago by
Tim Peters
▴ 170 • written 4 weeks ago by
s.malik
• 0
3
votes
3
replies
323
views
permutation test in edgeR
rna-seq
edgeR
updated 12 days ago by
Gordon Smyth
50k • written 24 days ago by
Netanel
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 2 days ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 19 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
1
vote
6
replies
481
views
GSVA on separate healthy and disease datasets
GSVA
updated 22 days ago by
James W. MacDonald
65k • written 23 days ago by
Lucy
▴ 60
1
vote
4
replies
215
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 10 days ago by
James W. MacDonald
65k • written 14 days ago by
Mirella Aurora
• 0
2
votes
2
replies
180
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 13 days ago by
James W. MacDonald
65k • written 14 days ago by
sansan
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 29 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 27 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 10 days ago
shepherl
3.9k
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
1
vote
10
replies
445
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 23 days ago
Kurtis
• 0
4
votes
8
replies
386
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 14 days ago by
Peter Hickey
▴ 740 • written 21 days ago by
Juan Higareda
• 0
1
vote
3
replies
343
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 17 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
0
votes
4
replies
260
views
DEG with low counts
DESeq2
updated 13 days ago by
Michael Love
41k • written 18 days ago by
Rajat
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago
Chris
• 0
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
22 days ago • updated 13 days ago
Weiqian
▴ 10
0
votes
1
reply
148
views
Adding columns to DEXSeqResults object
DEXSeq
updated 14 days ago by
Alejandro Reyes
★ 1.9k • written 16 days ago by
Clyde
• 0
0
votes
2
replies
91
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 14 hours ago
Ian D.
▴ 70
0
votes
1
reply
130
views
Bioinformatics student
Des
DESeq2
updated 20 days ago by
hemantcnaik
• 0 • written 20 days ago by
Sahar
• 0
5
votes
9
replies
899
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
22 days ago • updated 14 days ago
Chris
• 0
1
vote
4
replies
456
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 1 day ago
JKim
• 0
1
vote
4
replies
195
views
minfi::read.metharray.exp
minfiData
minfi
updated 8 days ago by
Basti
▴ 780 • written 10 days ago by
clacarion
• 0
0
votes
1
reply
114
views
ATACseq merge peaks
DiffBind
updated 6 days ago by
ATpoint
★ 4.1k • written 8 days ago by
Shloka
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 15 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
1
vote
3
replies
241
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
Shaimaa Gamal
• 0
0
votes
7
replies
294
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
15 days ago • updated 9 days ago
hortense96
• 0
1
vote
2
replies
490
views
GSVA error
GSVA
18 days ago • updated 17 days ago
Alex
• 0
2
votes
9
replies
343
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
Alexandre
• 0
1
vote
1
reply
151
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by
Gordon Smyth
50k • written 10 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
3
replies
178
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
prity6459
• 0
0
votes
2
replies
161
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
joshua.mannheimer
• 0
0
votes
5
replies
285
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 8 days ago by
James W. MacDonald
65k • written 11 days ago by
Gayatri
• 0
0
votes
1
reply
133
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 22 days ago by
ATpoint
★ 4.1k • written 24 days ago by
Merav
• 0
0
votes
2
replies
159
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
29 days ago
Marianna
▴ 20
0
votes
2
replies
196
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
2 days ago • updated 1 day ago
Yveto
• 0
0
votes
1
reply
87
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
Dev
• 0
205 results • Page
1 of 5
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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