Showing : edger • reset
2
votes
4
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450
views
EdgeR Biological CVs
edgeR
updated 27 days ago by 52k • written 4 weeks ago by • 0
3
votes
5
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934
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 4 weeks ago by 68k • written 4 weeks ago by ▴ 10
0
votes
2
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299
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
6 weeks ago gingergeiger22 • 0
0
votes
1
reply
378
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 6 weeks ago by 43k • written 8 weeks ago by • 0
1
vote
8
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947
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
7 weeks ago • updated 6 weeks ago Andre • 0
1
vote
9
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874
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 9 weeks ago by ▴ 30
6
votes
10
replies
2.7k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 10 weeks ago by ★ 4.7k • written 12 weeks ago by ▴ 10
7
votes
6
replies
974
views
ANOVA like approach of edgeR
edgeR
updated 12 weeks ago by 52k • written 3 months ago by ▴ 10
3
votes
3
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605
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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
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 3 months 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
541
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
1.0k
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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703
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
3 months ago Philippine • 0
4
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6
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1.2k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
4 months ago • updated 3 months ago altintas.ali • 0
1
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2
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380
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
4 months ago Hongjian • 0
3
votes
3
replies
384
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
4 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
416
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 4 months ago by 52k • written 4 months ago by • 0
1
vote
1
reply
309
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 4 months ago by ★ 4.7k • written 4 months ago by • 0
1
vote
2
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559
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 4 months ago by 43k • written 5 months ago by ▴ 10
0
votes
2
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460
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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
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404
views
Inconsistent result in edgeR
edgeR
5 months ago hiroko.ohmiya • 0
1
vote
1
reply
535
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
946
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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
632
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 6 months ago by • 0
1
vote
1
reply
1.0k
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
448
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
657
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Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 6 months ago by 68k • written 6 months ago by ▴ 50
0
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4
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688
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 7 months ago by • 0
1
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8
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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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2.1k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 months ago by • 0 • written 11 months ago by ▴ 60
0
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4
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710
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
8 months ago vohara4 • 0
3
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6
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933
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
8 months ago JG13 • 0
3
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2
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778
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
9 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
834
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
738
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 9 months ago by 52k • written 9 months ago by • 0
0
votes
1
reply
443
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
4
votes
2
replies
1.3k
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
967
views
Citation for edgeR user guide
edgeR
written 10 months ago by ▴ 30
4
votes
6
replies
1.2k
views
FilterByExpr low counts with small sample size
edgeR
10 months ago Jonathan ▴ 10
0
votes
2
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450
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
10 months ago prity6459 • 0
0
votes
3
replies
672
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 9 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 10 months ago by • 0
1
vote
3
replies
719
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 10 months ago by 52k • written 10 months ago by • 0
5
votes
6
replies
985
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 10 months ago by ★ 4.7k • written 10 months ago by ▴ 70
1
vote
3
replies
617
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
624
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
10 months ago Marianna ▴ 20
0
votes
4
replies
1.0k
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
1.6k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 10 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: EuroBioC2023 abstract submission is open! by cirwin009 • 0
Submit here https://openreview.net/group?id=bioconductor.org/EuroBioC/2023/ [Block Blast][1] This article offers a thorough and in-depth…
Comment: How to formulate 2 factor nested design in DESeq2 by Mariane • 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
Comment: batch effect removal for agilent microarray data by gaye.yilmaz • 0
Thank you
Answer: Pathview visualisation not including positive log2 fold changes by James W. MacDonald 68k
Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
Comment: Differential variance analysis - can i use deseq2 by Marwan • 0
Thanks Michael for your answer, i didnt mean to use Deseq2 directly for the variance testing, but more like asking if using the (VST) data…
Votes
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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