Showing : EDGER • reset
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 7 hours ago by ★ 4.5k • written 23 hours ago by ▴ 10
7
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6
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641
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ANOVA like approach of edgeR
edgeR
updated 1 day ago by 52k • written 6 days ago by ▴ 10
3
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3
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467
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 8 days ago by 52k • written 8 days ago by • 0
2
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4
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1.5k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 17 days ago by 52k • written 21 days ago by • 0
1
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8
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1.0k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 24 days ago by • 0
0
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1
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427
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single cell RNA seq pseudobulk batch correction
edgeR
updated 27 days ago by 67k • written 27 days ago by • 0
3
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3
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843
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 4 weeks ago by • 0
0
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4
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573
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
4 weeks ago Philippine • 0
4
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6
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1.1k
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
5 weeks ago • updated 4 weeks ago altintas.ali • 0
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295
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edgeR 4.2.2 not compiled for Windows
edger edgeR
6 weeks ago Hongjian • 0
3
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3
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283
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
6 weeks ago Guido Hooiveld ★ 4.1k
4
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1
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309
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edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 6 weeks ago by 52k • written 7 weeks ago by • 0
1
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1
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231
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 8 weeks ago by ★ 4.5k • written 8 weeks ago by • 0
1
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2
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441
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 8 weeks ago by 43k • written 9 weeks ago by ▴ 10
0
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337
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 8 weeks ago by 52k • written 9 weeks ago by • 0
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2
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313
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Inconsistent result in edgeR
edgeR
10 weeks ago hiroko.ohmiya • 0
1
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1
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431
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Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 11 weeks ago by 52k • written 12 weeks ago by • 0
2
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9
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792
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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
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3
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484
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 3 months ago by • 0
1
vote
1
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623
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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
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1
reply
360
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 3 months ago by 52k • written 3 months ago by • 0
3
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3
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547
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Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 3 months ago by 67k • written 3 months ago by ▴ 50
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4
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560
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 4 months ago by • 0
1
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8
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934
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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
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5
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1.6k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 5 months ago by • 0 • written 8 months ago by ▴ 50
0
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4
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586
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
5 months ago vohara4 • 0
3
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6
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820
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Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
5 months ago JG13 • 0
3
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2
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634
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 months ago mohammedtoufiq91 ▴ 10
3
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3
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684
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
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3
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625
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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
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1
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381
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
4
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2
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1.1k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
7 months ago • updated 6 months ago gene_bioconductor ▴ 10
1
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2
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721
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Citation for edgeR user guide
edgeR
written 7 months ago by ▴ 30
4
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6
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982
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FilterByExpr low counts with small sample size
edgeR
7 months ago Jonathan ▴ 10
0
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2
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372
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
7 months ago prity6459 • 0
0
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3
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551
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 7 months ago by 52k • written 7 months ago by • 0
5
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3
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842
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Log-cpm values from limma
limma edgeR RNASeq
updated 6 months ago by 52k • written 7 months ago by • 0
3
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3
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861
views
permutation test in edgeR
rna-seq edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
1
vote
3
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626
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
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6
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854
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 7 months ago by ★ 4.5k • written 7 months ago by ▴ 70
1
vote
3
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545
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
0
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2
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516
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 months ago Marianna ▴ 20
0
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4
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831
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
8 months ago Lucy ▴ 60
3
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5
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1.2k
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
6
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705
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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
566
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
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5
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1.7k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 29 days ago by 52k • written 8 months ago by ▴ 50
2
votes
3
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575
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
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2
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563
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 months ago by 52k • written 8 months ago by • 0
2
votes
2
replies
540
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between lane normalization upper quantile
EDASeq edgeR
8 months ago elesofi • 0
50 results • Page 1 of 1
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Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.5k
Probably nf-core did not run with bootstrap/gibbs replicates. Check the code. See salmon docs on how to turn that on.
Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10
@atpoint Thank you. I did wanted to try using the `quant.sf` files from the `salmon` run by referring edgeR user guide example `4.6 Differe…
Comment: athPkgBuilder data source :missing probesets by bobihanigujjar • 0
In this article, we'll explore the demand for unbranded BJJ Gis and the benefits of choosing unbranded Gis for customization. [does anyone …
Comment: Crossover design with limma by SamGG ▴ 360
IMHO, here are the missing annotations treatmentdrug_orderDrugPlac - treatmentplacebo_orderDrugPlac, # effect of drug for the Drug…
Answer: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.5k
You don't need any of these files. You need the `catchSalmon` function which reads `quant.sf` and the inferential (Bootstrap/Gibbs) replica…
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Comment: ANOVA like approach of edgeR
Comment: Crossover design with limma
Answer: DESeq2 normalization vs VST vs rlog
Comment: makeContrastsDream for Interaction
Answer: Limma- Print-tip loess normalisation-printer layout information does not match M
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