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Showing :
questions
3
votes
6
replies
215
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
9 days ago • updated 8 days ago
nhaus
▴ 30
0
votes
2
replies
184
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 10 days ago by
Michael Love
41k • written 14 days ago by
nhaus
▴ 30
5
votes
6
replies
383
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 7 days ago by
ATpoint
★ 4.0k • written 10 days ago by
nhaus
▴ 30
0
votes
5
replies
460
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation
locateVariant
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
nhaus
▴ 30
0
votes
3
replies
1.3k
views
getLDS causes "biomaRt has encountered an unexpected server error"
biomaRt
written 12 months ago by
nhaus
▴ 30
1
vote
1
reply
644
views
Pseudobulk running all groups together vs subsetting first
DESeq2
edgeR
SingleCell
updated 14 months ago by
Wolfgang Huber
★ 13k • written 14 months ago by
nhaus
▴ 30
0
votes
1
reply
590
views
GSA type of input data
GSEA
GSA
vst
updated 15 months ago by
Michael Love
41k • written 15 months ago by
nhaus
▴ 30
7
votes
6
replies
2.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 15 months ago by
Gordon Smyth
50k • written 16 months ago by
nhaus
▴ 30
2
votes
1
reply
1.2k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma
BatchEffect
updated 22 months ago by
Gordon Smyth
50k • written 22 months ago by
nhaus
▴ 30
2
votes
3
replies
1.6k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 8 months ago by
James W. MacDonald
65k • written 23 months ago by
nhaus
▴ 30
2
votes
5
replies
1.7k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi
Microarray
23 months ago
nhaus
▴ 30
0
votes
0
replies
521
views
Using geNetClassifier with RNA seq data
geNetClassifier
Normalization
2.0 years ago
nhaus
▴ 30
0
votes
2
replies
1.9k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub
Install
updated 2.1 years ago by
shepherl
3.8k • written 2.1 years ago by
nhaus
▴ 30
9
votes
13
replies
6.3k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 10 weeks ago by
ATpoint
★ 4.0k • written 2.1 years ago by
nhaus
▴ 30
2
votes
3
replies
888
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma
DifferentialExpression
2.1 years ago
nhaus
▴ 30
1
vote
1
reply
1.1k
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 2.2 years ago by
ATpoint
★ 4.0k • written 2.2 years ago by
nhaus
▴ 30
4
votes
5
replies
1.7k
views
What to do if covariates in design matrix of limma are confounded
limma
DifferentialExpression
updated 23 months ago by
Sneha
• 0 • written 2.2 years ago by
nhaus
▴ 30
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