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18
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 10 days ago
shepherl
3.8k
0
votes
7
replies
640
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 4 days ago
shepherl
3.8k
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 25 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 23 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
4
votes
8
replies
360
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 9 days ago by
Peter Hickey
▴ 740 • written 16 days ago by
Juan Higareda
• 0
0
votes
4
replies
206
views
Storing directories inside an ExperimentHub package?
ExperimentHub
17 days ago • updated 16 days ago
Tim Barry
• 0
0
votes
2
replies
220
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
4 weeks ago • updated 25 days ago
w.cookson
• 0
3
votes
3
replies
295
views
permutation test in edgeR
rna-seq
edgeR
updated 7 days ago by
Gordon Smyth
50k • written 20 days ago by
Netanel
• 0
1
vote
4
replies
173
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 5 days ago by
James W. MacDonald
65k • written 9 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 24 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
6
votes
16
replies
2.3k
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
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 9 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
0
votes
3
replies
111
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
bas_work
▴ 30
0
votes
4
replies
236
views
DEG with low counts
DESeq2
updated 8 days ago by
Michael Love
41k • written 13 days ago by
Rajat
• 0
1
vote
3
replies
328
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 12 days ago by
Gordon Smyth
50k • written 18 days ago by
Simran
• 0
0
votes
4
replies
158
views
flowStats Search Error
flowStats
updated 11 days ago by
shepherl
3.8k • written 12 days ago by
tholmes
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 9 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
6
replies
329
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 29 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Faisal
• 0
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 25 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 5 days ago
shepherl
3.8k
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 6 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
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 14 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
0
votes
6
replies
317
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 17 days ago by
Tim Peters
▴ 170 • written 25 days ago by
s.malik
• 0
1
vote
10
replies
411
views
Obtaining pheno data from CEL files
GEO
affy
25 days ago • updated 18 days ago
Kurtis
• 0
12
votes
13
replies
854
views
Why p value inconsistent when using different number of pathway score?
limma
7 days ago • updated 12 hours ago
Chris
• 0
1
vote
6
replies
465
views
GSVA on separate healthy and disease datasets
GSVA
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
Lucy
▴ 60
2
votes
2
replies
150
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 8 days ago by
James W. MacDonald
65k • written 9 days ago by
sansan
• 0
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 22 days ago by
Michael
▴ 10 • written 24 months ago by
axe880
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
218
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 24 days ago by
Tim Peters
▴ 170 • written 24 days ago by
Kim
• 0
0
votes
1
reply
159
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 26 days ago by
Michael Love
41k • written 29 days ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
70
views
ATACseq merge peaks
DiffBind
updated 1 day ago by
ATpoint
★ 4.0k • written 3 days ago by
Shloka
• 0
0
votes
1
reply
93
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 9 days ago by
Michael Love
41k • written 9 days ago by
09191919
• 0
3
votes
5
replies
353
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 28 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Fabian
• 0
0
votes
1
reply
124
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 17 days ago by
ATpoint
★ 4.0k • written 19 days ago by
Merav
• 0
0
votes
2
replies
892
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 10 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
2
replies
446
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
10 days ago • updated 1 day ago
ussarizona
▴ 10
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 10 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
1
vote
2
replies
116
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
11 days ago
Ana
• 0
1
vote
3
replies
131
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 1 day ago by
Michael Love
41k • written 2 days ago by
JalapenoCornbread
• 0
3
votes
3
replies
179
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
15 days ago • updated 9 days ago
jacques.imbert
• 0
1
vote
3
replies
231
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
Shaimaa Gamal
• 0
5
votes
9
replies
870
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
17 days ago • updated 9 days ago
Chris
• 0
1
vote
3
replies
147
views
Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
andrebolerbarros
▴ 20
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 27 days ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
0
votes
4
replies
291
views
Help with design.matrix
limma
22 days ago • updated 21 days ago
andrea.rodriguez-martinez13
• 0
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 24 days ago by
Michael Love
41k • written 24 days ago by
RL
• 0
1
vote
1
reply
68
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 1 day ago by
Leo Lahti
▴ 40 • written 1 day ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
94
views
FDR via q-value
qvalue
updated 5 days ago by
James W. MacDonald
65k • written 8 days ago by
John
• 0
193 results • Page
1 of 4
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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