Showing : edger • reset
4
votes
8
replies
1.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 2 days ago by 52k • written 4 days ago by ▴ 10
7
votes
6
replies
760
views
ANOVA like approach of edgeR
edgeR
updated 5 days ago by 52k • written 10 days ago by ▴ 10
3
votes
3
replies
484
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 12 days ago by 52k • written 12 days ago by • 0
2
votes
4
replies
1.6k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 21 days ago by 52k • written 25 days ago by • 0
1
vote
8
replies
1.0k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 28 days ago by • 0
0
votes
1
reply
434
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 4 weeks ago by 67k • written 4 weeks ago by • 0
3
votes
3
replies
852
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 5 weeks ago by • 0
0
votes
4
replies
583
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
5 weeks ago Philippine • 0
4
votes
6
replies
1.1k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
6 weeks ago • updated 5 weeks ago altintas.ali • 0
1
vote
2
replies
298
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
6 weeks ago Hongjian • 0
3
votes
3
replies
287
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
7 weeks ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
314
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 7 weeks ago by 52k • written 8 weeks ago by • 0
1
vote
1
reply
238
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
1
vote
2
replies
448
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 9 weeks ago by 43k • written 10 weeks ago by ▴ 10
0
votes
2
replies
343
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 9 weeks ago by 52k • written 9 weeks ago by • 0
1
vote
2
replies
317
views
Inconsistent result in edgeR
edgeR
10 weeks ago hiroko.ohmiya • 0
1
vote
1
reply
440
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 12 weeks ago by 52k • written 12 weeks ago by • 0
2
votes
9
replies
809
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 3 months ago by 52k • written 3 months ago by • 0
0
votes
3
replies
493
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 3 months ago by • 0
1
vote
1
reply
640
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 3 months ago by ★ 28k • written 3 months ago by • 0
0
votes
1
reply
369
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 3 months ago by 52k • written 3 months ago by • 0
3
votes
3
replies
557
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 3 months ago by 67k • written 3 months ago by ▴ 50
0
votes
4
replies
569
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 4 months ago by • 0
1
vote
8
replies
949
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 4 months ago by 52k • written 5 months ago by • 0
3
votes
5
replies
1.6k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 5 months ago by • 0 • written 9 months ago by ▴ 50
0
votes
4
replies
593
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
5 months ago vohara4 • 0
3
votes
6
replies
821
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
6 months ago JG13 • 0
3
votes
2
replies
650
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
698
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 6 months ago by 52k • written 6 months ago by • 0
1
vote
3
replies
634
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 months ago by 52k • written 6 months ago by • 0
0
votes
1
reply
384
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
4
votes
2
replies
1.1k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
7 months ago gene_bioconductor ▴ 10
1
vote
2
replies
729
views
Citation for edgeR user guide
edgeR
written 7 months ago by ▴ 30
4
votes
6
replies
998
views
FilterByExpr low counts with small sample size
edgeR
7 months ago Jonathan ▴ 10
0
votes
2
replies
376
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
7 months ago prity6459 • 0
0
votes
3
replies
560
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 7 months ago by 52k • written 7 months ago by • 0
5
votes
3
replies
864
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 months ago by 52k • written 7 months ago by • 0
3
votes
3
replies
873
views
permutation test in edgeR
rna-seq edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
1
vote
3
replies
632
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 7 months ago by 52k • written 7 months ago by • 0
5
votes
6
replies
859
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 7 months ago by ★ 4.6k • written 7 months ago by ▴ 70
1
vote
3
replies
547
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 8 months ago by 67k • written 8 months ago by • 0
0
votes
2
replies
522
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
8 months ago Marianna ▴ 20
0
votes
4
replies
840
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
8 months ago Lucy ▴ 60
3
votes
5
replies
1.2k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
6
replies
712
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
1
reply
576
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
6
votes
5
replies
1.7k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 4 weeks ago by 52k • written 8 months ago by ▴ 50
2
votes
3
replies
583
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
2
replies
566
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 months ago by 52k • written 8 months ago by • 0
2
votes
2
replies
555
views
between lane normalization upper quantile
EDASeq edgeR
8 months ago elesofi • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
Hi, what's the output from `dim(spe)`?
Answer: DESeq2- merging technical vs biological replicates by Michael Love 43k
Technical replicates (more sequencing of same library) you can use `collapseReplicates()`. But biological replicates are best handled wi…
Answer: lfcShrink and alpha value by Michael Love 43k
`summary()` is just printing a particular `alpha`, but you can do: ``` summary(res, alpha = ...) ```
Answer: DESeq2 dispersion estimates fitting drastically different based on explanatory v by Michael Love 43k
> DESeq2 treats this as a numeric variable with a range from 19560-19660 And it gives a warning to not use this type of covariate, which…
Votes
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Transcript-level differential expression using DESeq2
Comment: What type of counts data to import for performing Isoform analysis in edgeR
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