Showing : edger • reset
2
votes
5
replies
332
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 22 hours ago by 67k • written 1 day ago by ▴ 10
0
votes
2
replies
195
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
12 days ago • updated 10 days ago gingergeiger22 • 0
0
votes
1
reply
330
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 13 days ago by 43k • written 24 days ago by • 0
1
vote
8
replies
787
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
17 days ago • updated 9 days ago Andre • 0
1
vote
9
replies
777
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 weeks ago by ▴ 30
6
votes
10
replies
2.5k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 5 weeks ago by ★ 4.6k • written 7 weeks ago by ▴ 10
7
votes
6
replies
904
views
ANOVA like approach of edgeR
edgeR
updated 7 weeks ago by 52k • written 8 weeks ago by ▴ 10
3
votes
3
replies
570
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 8 weeks ago by 52k • written 8 weeks ago by • 0
2
votes
4
replies
1.7k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 9 weeks ago by 52k • written 10 weeks ago by • 0
1
vote
8
replies
1.2k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 10 weeks ago by • 0
0
votes
1
reply
478
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 10 weeks ago by 67k • written 10 weeks ago by • 0
3
votes
3
replies
944
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 11 weeks ago by • 0
0
votes
4
replies
655
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
11 weeks ago Philippine • 0
4
votes
6
replies
1.2k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
3 months ago • updated 11 weeks ago altintas.ali • 0
1
vote
2
replies
342
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
3 months ago Hongjian • 0
3
votes
3
replies
342
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
3 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
375
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
279
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
506
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 3 months ago by ▴ 10
0
votes
2
replies
413
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 3 months ago by 52k • written 3 months ago by • 0
1
vote
2
replies
366
views
Inconsistent result in edgeR
edgeR
4 months ago hiroko.ohmiya • 0
1
vote
1
reply
488
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
votes
9
replies
881
views
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
votes
3
replies
562
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 5 months ago by • 0
1
vote
1
reply
810
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
415
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
616
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 5 months ago by 67k • written 5 months ago by ▴ 50
0
votes
4
replies
630
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
1
vote
8
replies
1.1k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 6 months ago by 52k • written 6 months ago by • 0
3
votes
5
replies
1.9k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 6 months ago by • 0 • written 10 months ago by ▴ 50
0
votes
4
replies
653
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
7 months ago vohara4 • 0
3
votes
6
replies
885
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
7 months ago JG13 • 0
3
votes
2
replies
712
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
8 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
767
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
689
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
votes
1
reply
413
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
862
views
Citation for edgeR user guide
edgeR
written 8 months ago by ▴ 30
4
votes
6
replies
1.1k
views
FilterByExpr low counts with small sample size
edgeR
9 months ago Jonathan ▴ 10
0
votes
2
replies
416
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
9 months ago prity6459 • 0
0
votes
3
replies
634
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 9 months ago by 52k • written 9 months ago by • 0
5
votes
3
replies
980
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
1.0k
views
permutation test in edgeR
rna-seq edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
1
vote
3
replies
679
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
941
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
583
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
581
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
9 months ago Marianna ▴ 20
0
votes
4
replies
920
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 9 months ago by • 0
0
votes
6
replies
794
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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