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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
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
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
4
replies
260
views
DEG with low counts
DESeq2
updated 13 days ago by
Michael Love
41k • written 18 days ago by
Rajat
• 0
0
votes
3
replies
143
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
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
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
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
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
0
votes
4
replies
182
views
flowStats Search Error
flowStats
updated 16 days ago by
shepherl
3.9k • written 17 days ago by
tholmes
• 0
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
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
3
votes
3
replies
319
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 24 days ago by
Netanel
• 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
0
votes
4
replies
220
views
Storing directories inside an ExperimentHub package?
ExperimentHub
22 days ago • updated 21 days ago
Tim Barry
• 0
0
votes
2
replies
48
views
DESeq2 v1.35.0
DESeq2
updated 7 hours ago by
Michael Love
41k • written 8 hours ago by
Espresso
• 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
1
vote
10
replies
444
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 23 days ago
Kurtis
• 0
2
votes
2
replies
179
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
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 18 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
0
votes
6
replies
330
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 21 days ago by
Tim Peters
▴ 170 • written 4 weeks ago by
s.malik
• 0
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
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
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
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 29 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
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
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 10 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
2
votes
5
replies
240
views
get BM error
ensembldb
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
Fara
• 0
0
votes
1
reply
85
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
Dev
• 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
0
votes
3
replies
49
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
3 hours ago
arfranco
▴ 130
0
votes
1
reply
24
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 1 hour ago by
Gordon Smyth
50k • written 5 hours ago by
c53aba27
• 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
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
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 13 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
2
votes
2
replies
167
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
20 days ago • updated 17 days ago
daniel.carbajo
• 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
1
vote
1
reply
108
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 6 days ago by
Leo Lahti
▴ 40 • written 6 days ago by
Dario Strbenac
★ 1.5k
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
2
replies
124
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
13 days ago
prity6459
• 0
3
votes
3
replies
197
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
3
votes
1
reply
297
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
i.sudbery
▴ 40
1
vote
2
replies
189
views
Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago
hemantcnaik
• 0
0
votes
1
reply
106
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 14 days ago by
Michael Love
41k • written 14 days ago by
09191919
• 0
0
votes
1
reply
157
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 23 days ago by
Michael Love
41k • written 23 days ago by
Adelaide
• 0
0
votes
7
replies
292
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
15 days ago • updated 9 days ago
hortense96
• 0
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 27 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
206 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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