Showing : EDGER • reset
2
votes
4
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377
views
EdgeR Biological CVs
edgeR
updated 14 days ago by 52k • written 18 days ago by • 0
2
votes
5
replies
728
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 21 days ago by 68k • written 21 days ago by ▴ 10
0
votes
2
replies
281
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
4 weeks ago gingergeiger22 • 0
0
votes
1
reply
369
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 4 weeks ago by 43k • written 6 weeks ago by • 0
1
vote
8
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920
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
5 weeks ago • updated 4 weeks ago Andre • 0
1
vote
9
replies
853
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 7 weeks ago by ▴ 30
6
votes
10
replies
2.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 8 weeks ago by ★ 4.6k • written 10 weeks ago by ▴ 10
7
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6
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954
views
ANOVA like approach of edgeR
edgeR
updated 10 weeks ago by 52k • written 10 weeks ago by ▴ 10
3
votes
3
replies
583
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 11 weeks ago by 52k • written 11 weeks ago by • 0
2
votes
4
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1.7k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 12 weeks ago by 52k • written 3 months ago by • 0
1
vote
8
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1.3k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 3 months ago by • 0
0
votes
1
reply
519
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 3 months ago by 68k • written 3 months ago by • 0
3
votes
3
replies
982
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 3 months ago by • 0
0
votes
4
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685
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
3 months ago Philippine • 0
4
votes
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 altintas.ali • 0
1
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2
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365
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
3 months ago Hongjian • 0
3
votes
3
replies
370
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
3 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
398
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 3 months ago by 52k • written 4 months ago by • 0
1
vote
1
reply
296
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 4 months ago by ★ 4.6k • written 4 months ago by • 0
1
vote
2
replies
543
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
votes
2
replies
449
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 4 months ago by 52k • written 4 months ago by • 0
1
vote
2
replies
390
views
Inconsistent result in edgeR
edgeR
4 months ago hiroko.ohmiya • 0
1
vote
1
reply
513
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 5 months ago by 52k • written 5 months ago by • 0
2
votes
9
replies
924
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 5 months ago by 52k • written 5 months ago by • 0
0
votes
3
replies
597
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 5 months ago by • 0
1
vote
1
reply
918
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 6 months ago by ★ 28k • written 6 months ago by • 0
0
votes
1
reply
437
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 6 months ago by 52k • written 6 months ago by • 0
3
votes
3
replies
642
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 6 months ago by 68k • written 6 months ago by ▴ 50
0
votes
4
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662
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 7 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 7 months ago by 52k • written 7 months ago by • 0
3
votes
5
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2.0k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 months ago by • 0 • written 11 months ago by ▴ 60
0
votes
4
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695
views
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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911
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
8 months ago JG13 • 0
3
votes
2
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746
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
814
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
722
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
435
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 9 months ago by 52k • written 9 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
9 months ago gene_bioconductor ▴ 10
1
vote
2
replies
923
views
Citation for edgeR user guide
edgeR
written 9 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
437
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
9 months ago prity6459 • 0
0
votes
3
replies
657
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
1.0k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 9 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 10 months ago by • 0
1
vote
3
replies
705
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 9 months ago by 52k • written 10 months ago by • 0
5
votes
6
replies
971
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 9 months ago by ★ 4.6k • written 10 months ago by ▴ 70
1
vote
3
replies
604
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
2
replies
611
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
10 months ago Marianna ▴ 20
0
votes
4
replies
969
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
10 months ago Lucy ▴ 60
3
votes
6
replies
1.5k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 10 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: error in ChAMP loading file by 81becky • 0
hi Giulia, it sounds like you're facing a frustating issue with your chAMP import. One common suggestion is to double-check your CSV fomat…
Answer: DESeq2 adujsted p-value cutoff seemingly not working by James W. MacDonald 68k
From `?results' ``` On p-values: By default, independent filtering is performed to select a set of genes for multiple tes…
Comment: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by SofieK • 0
Thank you, I will try this and see.
Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexploitss • 0
Data input is the adding of data into a computer. This can take place through an input device such as a keyboard. A user inputs data, which…
Comment: GenomeInfoDbData cannot install in R and warning had non-zero exit status by Renuka • 0
how you did it pls explain
Votes
A: Effect of lfcThreshold on p-value in DESeq2
Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode =
Comment: Unused arguments error without used arguments in GSVA?
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