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Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
20 months ago
Patadù
▴ 20
0
votes
4
replies
1.5k
views
error running enricher from clusterprofiler
clusterProfiler
cluster
20 months ago
Yael
• 0
3
votes
3
replies
1.2k
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Guillermo
• 0
2
votes
1
reply
829
views
How to design DEXSeq formula for multiple variables
DEXSeq
20 months ago • updated 19 months ago
Sara
• 0
4
votes
9
replies
1.4k
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
pangtaihin
• 0
0
votes
0
replies
547
views
Difference in Contrast in DiffBind
DiffBind
20 months ago
user_bioinfo
• 0
1
vote
2
replies
1.0k
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
20 months ago
Patadù
▴ 20
10
votes
11
replies
3.3k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 19 months ago by
Sara
• 0 • written 8.4 years ago by
Sylvain Foisy
▴ 80
0
votes
3
replies
820
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 20 months ago by
Michael Love
43k • written 20 months ago by
Kasper
• 0
0
votes
2
replies
2.3k
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 20 months ago by
zhouwanding
▴ 20 • written 20 months ago by
Seungmin
• 0
1
vote
0
replies
910
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
21 months ago • updated 20 months ago
shepherl
4.2k
1
vote
2
replies
1.0k
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
20 months ago
Daniel
• 0
0
votes
1
reply
804
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 20 months ago by
Michael Love
43k • written 20 months ago by
piemmea
• 0
1
vote
0
replies
1.1k
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
20 months ago
Aleena_Ensembl
▴ 30
1
vote
2
replies
686
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 20 months ago by
Researcher
▴ 10
0
votes
9
replies
2.4k
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 19 months ago by
BioinfGuru
▴ 70 • written 20 months ago by
Eric Katagirya
• 0
1
vote
3
replies
1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Ashley
• 0
3
votes
4
replies
993
views
Store output of matchPWM()
biostrings
Biostrings
20 months ago
mat149
▴ 80
1
vote
2
replies
1.2k
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
20 months ago
BioinfGuru
▴ 70
0
votes
2
replies
701
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
20 months ago
Yveto
• 0
0
votes
1
reply
1.6k
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 20 months ago by
Guido Hooiveld
★ 4.1k • written 20 months ago by
aogunbaw
• 0
0
votes
7
replies
2.1k
views
ChAMP installation issue
Cha
ChAMP
updated 19 months ago by
James W. MacDonald
68k • written 20 months ago by
e1271094
• 0
0
votes
1
reply
649
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
sajadahmad41454
• 0
1
vote
2
replies
1.1k
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
20 months ago
Dylan.Sheerin
• 0
0
votes
0
replies
371
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
20 months ago
neilzhao
▴ 30
0
votes
1
reply
744
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
sajadahmad41454
• 0
2
votes
7
replies
2.0k
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
20 months ago
sajadahmad41454
• 0
0
votes
0
replies
386
views
Treeio as.treedata function seq lenght error
treeio
20 months ago
nromerov
• 0
2
votes
2
replies
1.3k
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
20 months ago
user_bioinfo
• 0
3
votes
10
replies
2.1k
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Abbey
• 0
2
votes
4
replies
3.4k
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 6 months ago by
UlyssesHenson
• 0 • written 20 months ago by
e1271094
• 0
0
votes
1
reply
451
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 20 months ago by
shepherl
4.2k • written 20 months ago by
cyril.dalmasso
• 0
0
votes
0
replies
543
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
20 months ago
Dinesh
• 0
3
votes
5
replies
1.2k
views
Help with running egsea()
EGSEA
20 months ago
Chris
▴ 20
3
votes
1
reply
904
views
How to save the DEXSeq results
DEXSeq
updated 20 months ago by
Michael Love
43k • written 20 months ago by
Sara
• 0
4
votes
5
replies
2.0k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
20 months ago
Chris
▴ 20
0
votes
3
replies
857
views
Couldn't connect to server while using "pathways"
graphite
updated 20 months ago by
Michael Love
43k • written 20 months ago by
fduguchunhui
• 0
2
votes
1
reply
651
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 20 months ago by
Michael Love
43k • written 20 months ago by
mat149
▴ 80
2
votes
1
reply
864
views
Handling multiple differential expression comparisons
DESeq2
20 months ago • updated 19 months ago
Zainab
▴ 20
2
votes
2
replies
1.7k
views
fgsea significant result
fgsea
20 months ago
Chris
▴ 20
0
votes
44
replies
6.3k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 20 months ago by
Michael Love
43k • written 2.9 years ago by
Poonam
• 0
0
votes
6
replies
1.2k
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 20 months ago by
swbarnes2
★ 1.4k • written 20 months ago by
arfranco
▴ 130
3
votes
2
replies
1.1k
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 19 months ago by
Gordon Smyth
53k • written 20 months ago by
Kim
• 0
2
votes
3
replies
1.3k
views
package goseq seems to be not available on the latest version of R
goseq
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Patrycja
▴ 20
2
votes
6
replies
2.5k
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 10 months ago by
Jane
• 0 • written 20 months ago by
Reza
• 0
0
votes
1
reply
1.1k
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 14 months ago by
B.N
• 0 • written 20 months ago by
Henry
▴ 10
0
votes
1
reply
674
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
z_bahari
• 0
0
votes
1
reply
756
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
c53aba27
• 0
4
votes
2
replies
1.8k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
20 months ago
gene_bioconductor
▴ 10
0
votes
0
replies
440
views
flowStats for CyTOF
flowStats
20 months ago
tholmes
• 0
46,710 results • Page
24 of 935
Recent ...
Replies
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
Ludwig Geistlinger
▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
Votes
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
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