Showing : EdgeR • reset
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108
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 15 hours ago by ★ 4.7k • written 1 day ago by ▴ 20
0
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1
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171
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Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 6 days ago by 52k • written 6 days ago by • 0
0
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4
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1.1k
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DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 5 days ago by • 0 • written 10 days ago by • 0
2
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4
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487
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EdgeR Biological CVs
edgeR
updated 6 weeks ago by 52k • written 7 weeks ago by • 0
3
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5
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1.2k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 7 weeks ago by 68k • written 7 weeks ago by ▴ 10
0
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2
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319
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
9 weeks ago gingergeiger22 • 0
0
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1
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395
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
1
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8
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996
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Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
9 weeks ago • updated 8 weeks ago Andre • 0
1
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9
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917
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 11 weeks ago by ▴ 30
6
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10
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2.7k
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
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6
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1.0k
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ANOVA like approach of edgeR
edgeR
updated 3 months ago by 52k • written 3 months ago by ▴ 10
3
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3
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630
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 3 months ago by 52k • written 3 months ago by • 0
2
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4
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1.8k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 3 months ago by 52k • written 4 months ago by • 0
1
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8
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1.6k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
updated 19 hours ago by • 0 • written 4 months ago by • 0
0
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1
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569
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single cell RNA seq pseudobulk batch correction
edgeR
updated 4 months ago by 68k • written 4 months ago by • 0
3
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3
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1.1k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 4 months ago by • 0
0
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4
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731
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
4 months ago Philippine • 0
4
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6
replies
1.3k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
4 months ago altintas.ali • 0
1
vote
2
replies
409
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
4 months ago Hongjian • 0
3
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3
replies
409
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago • updated 4 months ago Guido Hooiveld ★ 4.1k
4
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1
reply
435
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
340
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
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2
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585
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 5 months ago by ▴ 10
0
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2
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494
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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
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2
replies
418
views
Inconsistent result in edgeR
edgeR
5 months ago hiroko.ohmiya • 0
1
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1
reply
558
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
993
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
676
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 7 months ago by • 0
1
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1
reply
1.1k
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
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1
reply
474
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
688
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 7 months ago by 68k • written 7 months ago by ▴ 50
0
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4
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723
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 8 months ago by • 0
1
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8
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1.2k
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
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5
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2.3k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 months ago by • 0 • written 12 months ago by ▴ 60
0
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4
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752
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
965
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
9 months ago JG13 • 0
3
votes
2
replies
815
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
9 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
866
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
1
vote
3
replies
767
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
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1
reply
459
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
4
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2
replies
1.3k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
10 months ago gene_bioconductor ▴ 10
1
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2
replies
1.0k
views
Citation for edgeR user guide
edgeR
written 10 months ago by ▴ 30
4
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6
replies
1.2k
views
FilterByExpr low counts with small sample size
edgeR
10 months ago Jonathan ▴ 10
0
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2
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463
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
10 months ago prity6459 • 0
0
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3
replies
702
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 10 months ago by 52k • written 10 months ago by • 0
5
votes
3
replies
1.1k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 10 months ago by 52k • written 10 months ago by • 0
3
votes
3
replies
1.2k
views
permutation test in edgeR
rna-seq edgeR
updated 10 months ago by 52k • written 11 months ago by • 0
1
vote
3
replies
739
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 10 months ago by 52k • written 11 months ago by • 0
5
votes
6
replies
1.1k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 11 months ago by ★ 4.7k • written 11 months ago by ▴ 70
1
vote
3
replies
643
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 11 months ago by 68k • written 11 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Hoover • 0
I got it! ([Drift Boss][1]) [1]: https://driftbossgame.co
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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