Showing : edger • reset
5
votes
3
replies
727
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 3 days ago by 52k • written 4 days ago by ▴ 10
2
votes
2
replies
1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
11 days ago • updated 5 days ago Elizabeth • 0
0
votes
2
replies
385
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 5 days ago by 43k • written 13 days ago by ▴ 20
0
votes
1
reply
191
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 18 days ago by 52k • written 18 days ago by • 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 17 days ago by • 0 • written 23 days ago by • 0
2
votes
4
replies
509
views
EdgeR Biological CVs
edgeR
updated 8 weeks ago by 52k • written 8 weeks ago by • 0
3
votes
5
replies
1.2k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 9 weeks ago by 68k • written 9 weeks ago by ▴ 10
0
votes
2
replies
345
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
11 weeks ago • updated 10 weeks ago gingergeiger22 • 0
0
votes
1
reply
413
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 11 weeks ago by 43k • written 12 weeks ago by • 0
1
vote
8
replies
1.0k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
11 weeks ago • updated 10 weeks ago Andre • 0
1
vote
9
replies
972
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
6
votes
10
replies
2.8k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 3 months ago by ★ 4.7k • written 3 months ago by ▴ 10
7
votes
6
replies
1.0k
views
ANOVA like approach of edgeR
edgeR
updated 3 months ago by 52k • written 4 months ago by ▴ 10
3
votes
3
replies
642
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 4 months ago by 52k • written 4 months ago by • 0
2
votes
4
replies
1.9k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 4 months ago by 52k • written 4 months ago by • 0
1
vote
8
replies
1.7k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 4 months ago by • 0
0
votes
1
reply
603
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 4 months ago by 68k • written 4 months ago by • 0
3
votes
3
replies
1.1k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 4 months ago by • 0
0
votes
4
replies
769
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
4 months ago Philippine • 0
4
votes
6
replies
1.4k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
5 months ago • updated 4 months ago altintas.ali • 0
1
vote
2
replies
430
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
5 months ago Hongjian • 0
3
votes
3
replies
436
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
452
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
1
vote
1
reply
351
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 months ago by ★ 4.7k • written 5 months ago by • 0
1
vote
2
replies
607
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 6 months ago by ▴ 10
0
votes
2
replies
511
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
1
vote
2
replies
438
views
Inconsistent result in edgeR
edgeR
6 months ago hiroko.ohmiya • 0
1
vote
1
reply
575
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 6 months ago by 52k • written 6 months ago by • 0
2
votes
9
replies
1.0k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 6 months ago by 52k • written 6 months ago by • 0
0
votes
3
replies
694
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 7 months ago by • 0
1
vote
1
reply
1.3k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 7 months ago by ★ 28k • written 7 months ago by • 0
0
votes
1
reply
483
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 7 months ago by 52k • written 7 months ago by • 0
3
votes
3
replies
706
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 7 months ago by 68k • written 7 months ago by ▴ 50
0
votes
4
replies
740
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 8 months ago by • 0
1
vote
8
replies
1.3k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 8 months ago by 52k • written 8 months ago by • 0
3
votes
5
replies
2.4k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 months ago by • 0 • written 12 months ago by ▴ 60
0
votes
4
replies
769
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
9 months ago vohara4 • 0
3
votes
6
replies
990
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
9 months ago JG13 • 0
3
votes
2
replies
835
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
10 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
879
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
1
vote
3
replies
789
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 10 months ago by 52k • written 10 months ago by • 0
0
votes
1
reply
469
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
4
votes
2
replies
1.4k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
10 months ago gene_bioconductor ▴ 10
1
vote
2
replies
1.1k
views
Citation for edgeR user guide
edgeR
written 11 months ago by ▴ 30
4
votes
6
replies
1.3k
views
FilterByExpr low counts with small sample size
edgeR
11 months ago Jonathan ▴ 10
0
votes
2
replies
473
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
11 months ago prity6459 • 0
0
votes
3
replies
722
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 11 months ago by 52k • written 11 months ago by • 0
5
votes
3
replies
1.2k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 10 months ago by 52k • written 11 months ago by • 0
3
votes
3
replies
1.3k
views
permutation test in edgeR
rna-seq edgeR
updated 11 months ago by 52k • written 11 months ago by • 0
1
vote
3
replies
749
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 11 months ago by 52k • written 11 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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