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1.6k
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Comment: Comment: Low logFCs using MAST for scRNA-seq
15 months ago nhaus ▴ 70
0
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2
replies
1.1k
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Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 8 months ago by • 0 • written 16 months ago by ▴ 70
0
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0
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794
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
16 months ago nhaus ▴ 70
2
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1
reply
817
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by ▴ 70
0
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1
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1.4k
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Comment: Comment: How to correct for known and surrogate variables in DESeq2?
19 months ago nhaus ▴ 70
2
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1
reply
1.3k
views
Answer: Answer: ComplexHeatmap: change the names of a HeatmapAnnotation object
19 months ago nhaus ▴ 70
0
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1
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1.5k
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Comment: Comment: Not fully paired differential gene expression analysis
19 months ago nhaus ▴ 70
0
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0
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1.6k
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Comment: Comment: Surrogate variable analysis for paired RNA seq experiment
19 months ago nhaus ▴ 70
0
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1
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1.6k
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Comment: Comment: Surrogate variable analysis for paired RNA seq experiment
19 months ago nhaus ▴ 70
0
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1
reply
1.6k
views
Comment: Comment: Surrogate variable analysis for paired RNA seq experiment
19 months ago nhaus ▴ 70
3
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6
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1.6k
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
19 months ago nhaus ▴ 70
0
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2
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1.5k
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Comment: Comment: Not fully paired differential gene expression analysis
19 months ago nhaus ▴ 70
0
votes
2
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822
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 19 months ago by 43k • written 20 months ago by ▴ 70
5
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6
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1.5k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 19 months ago by ★ 5.0k • written 19 months ago by ▴ 70
0
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1
reply
1.2k
views
Comment: Comment: locateVariant from VariantAnnotation returns wrong results
2.0 years ago nhaus ▴ 70
0
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1
reply
1.2k
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Comment: Comment: locateVariant from VariantAnnotation returns wrong results
2.0 years ago nhaus ▴ 70
0
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5
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1.2k
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 2.0 years ago by 68k • written 2.0 years ago by ▴ 70
0
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3
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2.8k
views
getLDS causes "biomaRt has encountered an unexpected server error"
biomaRt
written 2.6 years ago by ▴ 70
1
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1
reply
1.4k
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 2.8 years ago by ★ 13k • written 2.8 years ago by ▴ 70
0
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1
reply
4.7k
views
Comment: Comment: Implementation of the "original" GSEA algorithm in R
2.9 years ago nhaus ▴ 70
0
votes
1
reply
1.0k
views
GSA type of input data
GSEA GSA vst
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 70
7
votes
6
replies
4.7k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 2.9 years ago by 53k • written 3.0 years ago by ▴ 70
2
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1
reply
2.1k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 70
2
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3
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2.8k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 2.3 years ago by 68k • written 3.5 years ago by ▴ 70
0
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0
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3.8k
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Comment: Comment: Get corresponding gene id for probe id from Affymetrix array
3.6 years ago nhaus ▴ 70
0
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1
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3.8k
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Comment: Comment: Get corresponding gene id for probe id from Affymetrix array
3.6 years ago nhaus ▴ 70
2
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5
replies
3.8k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
3.6 years ago nhaus ▴ 70
0
votes
0
replies
894
views
Using geNetClassifier with RNA seq data
geNetClassifier Normalization
3.7 years ago nhaus ▴ 70
0
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1
reply
2.5k
views
Comment: Comment: AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is requi
3.7 years ago nhaus ▴ 70
0
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2
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2.5k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 3.7 years ago by 4.2k • written 3.7 years ago by ▴ 70
0
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1
reply
13k
views
Comment: Comment: GSEA many significant gene sets despite no differentially expressed genes
3.7 years ago nhaus ▴ 70
0
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1
reply
13k
views
Comment: Comment: GSEA many significant gene sets despite no differentially expressed genes
3.7 years ago nhaus ▴ 70
0
votes
1
reply
13k
views
Comment: Comment: GSEA many significant gene sets despite no differentially expressed genes
3.7 years ago nhaus ▴ 70
12
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13
replies
13k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 22 months ago by ★ 5.0k • written 3.7 years ago by ▴ 70
0
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1
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13k
views
Comment: Comment: GSEA many significant gene sets despite no differentially expressed genes
3.7 years ago nhaus ▴ 70
0
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0
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1.6k
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Comment: Comment: Including squared covariates to account for non-linear dependencies in different
3.7 years ago nhaus ▴ 70
3
votes
3
replies
1.6k
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
3.7 years ago nhaus ▴ 70
1
vote
1
reply
2.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by ▴ 70
0
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0
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2.5k
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Comment: Comment: What to do if covariates in design matrix of limma are confounded
3.8 years ago nhaus ▴ 70
0
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2
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2.5k
views
Comment: Comment: What to do if covariates in design matrix of limma are confounded
3.8 years ago nhaus ▴ 70
4
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5
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2.5k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 3.6 years ago by • 0 • written 3.8 years ago by ▴ 70
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