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0
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1.2k
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Comment: Comment: Low logFCs using MAST for scRNA-seq
3 months ago nhaus ▴ 70
0
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1
reply
559
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Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 4 months ago by ★ 4.6k • written 4 months ago by ▴ 70
0
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0
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414
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
5 months ago nhaus ▴ 70
2
votes
1
reply
448
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 6 months ago by 67k • written 6 months ago by ▴ 70
0
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1
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979
views
Comment: Comment: How to correct for known and surrogate variables in DESeq2?
8 months ago nhaus ▴ 70
2
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1
reply
648
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Answer: Answer: ComplexHeatmap: change the names of a HeatmapAnnotation object
8 months ago nhaus ▴ 70
0
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1
reply
881
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Comment: Comment: Not fully paired differential gene expression analysis
8 months ago nhaus ▴ 70
0
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0
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873
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Comment: Comment: Surrogate variable analysis for paired RNA seq experiment
8 months ago nhaus ▴ 70
0
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1
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873
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Comment: Comment: Surrogate variable analysis for paired RNA seq experiment
8 months ago nhaus ▴ 70
0
votes
1
reply
873
views
Comment: Comment: Surrogate variable analysis for paired RNA seq experiment
8 months ago nhaus ▴ 70
3
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6
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873
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
8 months ago nhaus ▴ 70
0
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2
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881
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Comment: Comment: Not fully paired differential gene expression analysis
8 months ago nhaus ▴ 70
0
votes
2
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516
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 8 months ago by 43k • written 8 months ago by ▴ 70
5
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6
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881
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 8 months ago by ★ 4.6k • written 8 months ago by ▴ 70
0
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1
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834
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Comment: Comment: locateVariant from VariantAnnotation returns wrong results
12 months ago nhaus ▴ 70
0
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1
reply
834
views
Comment: Comment: locateVariant from VariantAnnotation returns wrong results
12 months ago nhaus ▴ 70
0
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5
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834
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 12 months ago by 67k • written 12 months ago by ▴ 70
0
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3
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2.1k
views
getLDS causes "biomaRt has encountered an unexpected server error"
biomaRt
written 20 months ago by ▴ 70
1
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1
reply
1000
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 22 months ago by ★ 13k • written 22 months ago by ▴ 70
0
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1
reply
3.1k
views
Comment: Comment: Implementation of the "original" GSEA algorithm in R
23 months ago nhaus ▴ 70
0
votes
1
reply
775
views
GSA type of input data
GSEA GSA vst
updated 23 months ago by 43k • written 23 months ago by ▴ 70
7
votes
6
replies
3.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 23 months ago by 52k • written 2.0 years ago by ▴ 70
2
votes
1
reply
1.7k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 2.5 years ago by 52k • written 2.5 years ago by ▴ 70
2
votes
3
replies
2.1k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 16 months ago by 67k • written 2.6 years ago by ▴ 70
0
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0
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2.6k
views
Comment: Comment: Get corresponding gene id for probe id from Affymetrix array
2.6 years ago nhaus ▴ 70
0
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1
reply
2.6k
views
Comment: Comment: Get corresponding gene id for probe id from Affymetrix array
2.6 years ago nhaus ▴ 70
2
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5
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2.6k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
2.6 years ago nhaus ▴ 70
0
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0
replies
696
views
Using geNetClassifier with RNA seq data
geNetClassifier Normalization
2.7 years ago nhaus ▴ 70
0
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1
reply
2.2k
views
Comment: Comment: AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is requi
2.7 years ago nhaus ▴ 70
0
votes
2
replies
2.2k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 2.7 years ago by 4.1k • written 2.7 years ago by ▴ 70
0
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1
reply
9.6k
views
Comment: Comment: GSEA many significant gene sets despite no differentially expressed genes
2.8 years ago nhaus ▴ 70
0
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1
reply
9.6k
views
Comment: Comment: GSEA many significant gene sets despite no differentially expressed genes
2.8 years ago nhaus ▴ 70
0
votes
1
reply
9.6k
views
Comment: Comment: GSEA many significant gene sets despite no differentially expressed genes
2.8 years ago nhaus ▴ 70
12
votes
13
replies
9.6k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 10 months ago by ★ 4.6k • written 2.8 years ago by ▴ 70
0
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1
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9.6k
views
Comment: Comment: GSEA many significant gene sets despite no differentially expressed genes
2.8 years ago nhaus ▴ 70
0
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0
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1.3k
views
Comment: Comment: Including squared covariates to account for non-linear dependencies in different
2.8 years ago nhaus ▴ 70
3
votes
3
replies
1.3k
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
2.8 years ago nhaus ▴ 70
1
vote
1
reply
1.5k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.8 years ago by ★ 4.6k • written 2.8 years ago by ▴ 70
0
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0
replies
2.1k
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Comment: Comment: What to do if covariates in design matrix of limma are confounded
2.8 years ago nhaus ▴ 70
0
votes
2
replies
2.1k
views
Comment: Comment: What to do if covariates in design matrix of limma are confounded
2.8 years ago nhaus ▴ 70
4
votes
5
replies
2.1k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 2.6 years ago by • 0 • written 2.8 years ago by ▴ 70
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