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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 14 days ago
shepherl
3.8k
0
votes
7
replies
682
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 8 days ago
shepherl
3.8k
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
0
votes
4
replies
220
views
Storing directories inside an ExperimentHub package?
ExperimentHub
21 days ago • updated 20 days ago
Tim Barry
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 13 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 28 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 26 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
0
votes
4
replies
181
views
flowStats Search Error
flowStats
updated 15 days ago by
shepherl
3.8k • written 16 days ago by
tholmes
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
4
votes
8
replies
382
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 13 days ago by
Peter Hickey
▴ 740 • written 21 days ago by
Juan Higareda
• 0
2
votes
2
replies
177
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
sansan
• 0
1
vote
10
replies
438
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 23 days ago
Kurtis
• 0
3
votes
3
replies
315
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 24 days ago by
Netanel
• 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
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 1 day ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
4
replies
259
views
DEG with low counts
DESeq2
updated 13 days ago by
Michael Love
41k • written 17 days ago by
Rajat
• 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
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 20 hours ago
Chris
• 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
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
0
votes
3
replies
133
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
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 10 days ago
shepherl
3.8k
1
vote
4
replies
212
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 9 days ago by
James W. MacDonald
65k • written 13 days ago by
Mirella Aurora
• 0
1
vote
6
replies
479
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
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
342
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
6
replies
324
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
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
1
reply
146
views
Adding columns to DEXSeqResults object
DEXSeq
updated 13 days ago by
Alejandro Reyes
★ 1.9k • written 15 days ago by
Clyde
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 14 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
1
reply
102
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 22 days ago by
Michael Love
41k • written 22 days ago by
Adelaide
• 0
1
vote
3
replies
240
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 27 days ago by
Shaimaa Gamal
• 0
1
vote
3
replies
200
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
andrebolerbarros
▴ 20
3
votes
3
replies
193
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
0
votes
1
reply
232
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 28 days ago by
Tim Peters
▴ 170 • written 28 days ago by
Kim
• 0
1
vote
2
replies
188
views
Design Matrix within group comparison more than two groups
DESeq2
19 days ago
hemantcnaik
• 0
3
votes
1
reply
293
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 8 days ago by
i.sudbery
▴ 40
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
1
vote
4
replies
451
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 21 hours ago
JKim
• 0
2
votes
9
replies
340
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
Alexandre
• 0
0
votes
1
reply
111
views
ATACseq merge peaks
DiffBind
updated 6 days ago by
ATpoint
★ 4.1k • written 7 days ago by
Shloka
• 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 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
102
views
Store output of matchPWM()
biostrings
Biostrings
updated 20 hours ago by
James W. MacDonald
65k • written 1 day ago by
mat149
▴ 70
0
votes
2
replies
159
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
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
0
votes
2
replies
121
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
13 days ago
prity6459
• 0
0
votes
1
reply
117
views
FDR via q-value
qvalue
updated 10 days ago by
James W. MacDonald
65k • written 12 days ago by
John
• 0
0
votes
3
replies
175
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
prity6459
• 0
201 results • Page
1 of 5
Recent ...
Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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