Showing : edgeR • reset
2
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4
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303
views
EdgeR Biological CVs
edgeR
updated 3 hours ago by 52k • written 3 days ago by • 0
2
votes
5
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697
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 6 days ago by 67k • written 6 days ago by ▴ 10
0
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2
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233
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
18 days ago • updated 16 days ago gingergeiger22 • 0
0
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1
reply
344
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 19 days ago by 43k • written 4 weeks ago by • 0
1
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8
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823
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Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
23 days ago • updated 15 days ago Andre • 0
1
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9
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811
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 5 weeks ago by ▴ 30
6
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10
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2.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 6 weeks ago by ★ 4.6k • written 8 weeks ago by ▴ 10
7
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6
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914
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ANOVA like approach of edgeR
edgeR
updated 8 weeks ago by 52k • written 8 weeks ago by ▴ 10
3
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3
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573
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 9 weeks ago by 52k • written 9 weeks ago by • 0
2
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4
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1.7k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 10 weeks ago by 52k • written 10 weeks ago by • 0
1
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8
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1.2k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 weeks ago by • 0
0
votes
1
reply
489
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 11 weeks ago by 67k • written 11 weeks ago by • 0
3
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3
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947
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 12 weeks ago by • 0
0
votes
4
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663
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
12 weeks ago Philippine • 0
4
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6
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1.2k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
3 months ago • updated 12 weeks ago altintas.ali • 0
1
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2
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350
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edgeR 4.2.2 not compiled for Windows
edger edgeR
3 months ago Hongjian • 0
3
votes
3
replies
349
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
3 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
380
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 3 months ago by 52k • written 3 months ago by • 0
1
vote
1
reply
283
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
1
vote
2
replies
513
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 4 months ago by ▴ 10
0
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2
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416
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 3 months ago by 52k • written 4 months ago by • 0
1
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2
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375
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Inconsistent result in edgeR
edgeR
4 months ago hiroko.ohmiya • 0
1
vote
1
reply
494
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 4 months ago by 52k • written 4 months ago by • 0
2
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9
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889
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 4 months ago by 52k • written 4 months ago by • 0
0
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3
replies
570
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 5 months ago by • 0
1
vote
1
reply
833
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 5 months ago by ★ 28k • written 5 months ago by • 0
0
votes
1
reply
423
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 5 months ago by 52k • written 5 months ago by • 0
3
votes
3
replies
619
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 5 months ago by 67k • written 5 months ago by ▴ 50
0
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4
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644
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
1
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8
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1.1k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 6 months ago by 52k • written 7 months ago by • 0
3
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5
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1.9k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 months ago by • 0 • written 10 months ago by ▴ 50
0
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4
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661
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
7 months ago vohara4 • 0
3
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6
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891
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Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
7 months ago JG13 • 0
3
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2
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718
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
8 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
776
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
1
vote
3
replies
699
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 8 months ago by 52k • written 8 months ago by • 0
0
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1
reply
421
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
4
votes
2
replies
1.2k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
8 months ago gene_bioconductor ▴ 10
1
vote
2
replies
877
views
Citation for edgeR user guide
edgeR
written 9 months ago by ▴ 30
4
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6
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1.1k
views
FilterByExpr low counts with small sample size
edgeR
9 months ago Jonathan ▴ 10
0
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2
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420
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
9 months ago prity6459 • 0
0
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3
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638
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 9 months ago by 52k • written 9 months ago by • 0
5
votes
3
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999
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 months ago by 52k • written 9 months ago by • 0
3
votes
3
replies
1.1k
views
permutation test in edgeR
rna-seq edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
1
vote
3
replies
684
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 9 months ago by 52k • written 9 months ago by • 0
5
votes
6
replies
952
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 9 months ago by ★ 4.6k • written 9 months ago by ▴ 70
1
vote
3
replies
589
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 9 months ago by 67k • written 9 months ago by • 0
0
votes
2
replies
588
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
9 months ago Marianna ▴ 20
0
votes
4
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931
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
9 months ago Lucy ▴ 60
3
votes
6
replies
1.4k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 10 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ? by Guido Hooiveld ★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Michael, Thank you very much!
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
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