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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
690
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 29 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 11 days ago
shepherl
3.9k
0
votes
4
replies
220
views
Storing directories inside an ExperimentHub package?
ExperimentHub
22 days ago • updated 21 days ago
Tim Barry
• 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
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
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 3 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
2
replies
182
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 14 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
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
6
replies
482
views
GSVA on separate healthy and disease datasets
GSVA
updated 23 days ago by
James W. MacDonald
65k • written 24 days ago by
Lucy
▴ 60
1
vote
10
replies
447
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 24 days ago
Kurtis
• 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
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
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
260
views
DEG with low counts
DESeq2
updated 14 days ago by
Michael Love
41k • written 18 days ago by
Rajat
• 0
0
votes
2
replies
61
views
DESeq2 v1.35.0
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Espresso
• 0
0
votes
4
replies
186
views
flowStats Search Error
flowStats
updated 16 days ago by
shepherl
3.9k • written 17 days ago by
tholmes
• 0
1
vote
4
replies
220
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 11 days ago by
James W. MacDonald
65k • written 14 days ago by
Mirella Aurora
• 0
0
votes
3
replies
145
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
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
6
replies
331
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
1
vote
3
replies
343
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 18 days ago by
Gordon Smyth
50k • written 23 days ago by
Simran
• 0
3
votes
3
replies
326
views
permutation test in edgeR
rna-seq
edgeR
updated 12 days ago by
Gordon Smyth
50k • written 25 days ago by
Netanel
• 0
4
votes
8
replies
387
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 14 days ago by
Peter Hickey
▴ 740 • written 22 days ago by
Juan Higareda
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
13 days ago • updated 1 day ago
Chris
• 0
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
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
0
votes
1
reply
154
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 13 hours ago by
Gordon Smyth
50k • written 22 hours ago by
gene_bioconductor
▴ 10
0
votes
5
replies
114
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 4 hours ago by
James W. MacDonald
65k • written 20 hours ago by
arfranco
▴ 130
1
vote
2
replies
499
views
GSVA error
GSVA
19 days ago • updated 18 days ago
Alex
• 0
2
votes
5
replies
244
views
get BM error
ensembldb
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
Fara
• 0
0
votes
3
replies
178
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 14 days ago by
Gordon Smyth
50k • written 15 days ago by
prity6459
• 0
1
vote
2
replies
985
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 10 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
4
replies
304
views
Help with design.matrix
limma
28 days ago • updated 27 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
106
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 15 days ago by
Michael Love
41k • written 15 days ago by
09191919
• 0
0
votes
2
replies
188
views
PCA plot suggestions
DESeq2
PCAtools
updated 7 days ago by
Michael Love
41k • written 8 days ago by
Aaliya
• 0
3
votes
1
reply
300
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
i.sudbery
▴ 40
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 28 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
0
votes
2
replies
90
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 18 hours ago
kcarey
• 0
0
votes
1
reply
130
views
Bioinformatics student
Des
DESeq2
updated 21 days ago by
hemantcnaik
• 0 • written 21 days ago by
Sahar
• 0
0
votes
7
replies
299
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
16 days ago • updated 10 days ago
hortense96
• 0
0
votes
1
reply
66
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 18 hours ago by
Gordon Smyth
50k • written 22 hours ago by
c53aba27
• 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
149
views
Adding columns to DEXSeqResults object
DEXSeq
updated 15 days ago by
Alejandro Reyes
★ 1.9k • written 16 days ago by
Clyde
• 0
1
vote
4
replies
431
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 28 days ago by
Gordon Smyth
50k • written 4 weeks ago by
jari.karppinen
• 0
0
votes
5
replies
286
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 9 days ago by
James W. MacDonald
65k • written 11 days ago by
Gayatri
• 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 28 days ago by
James W. MacDonald
65k • written 28 days ago by
joshua.mannheimer
• 0
0
votes
3
replies
122
views
Store output of matchPWM()
biostrings
Biostrings
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
mat149
▴ 70
203 results • Page
1 of 5
Recent ...
Replies
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
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…
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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