Showing : EdgeR • reset
1
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6
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266
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 2 days ago by 51k • written 4 days ago by • 0
3
votes
5
replies
796
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 days ago by • 0 • written 3 months ago by ▴ 50
0
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4
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249
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
18 days ago vohara4 • 0
3
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6
replies
507
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
26 days ago • updated 25 days ago JG13 • 0
2
votes
2
replies
248
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
5 weeks ago mohammedtoufiq91 ▴ 10
2
votes
3
replies
296
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 6 weeks ago by 51k • written 6 weeks ago by • 0
1
vote
3
replies
350
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 weeks ago by 51k • written 6 weeks ago by • 0
0
votes
1
reply
218
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 8 weeks ago by 51k • written 8 weeks ago by • 0
4
votes
2
replies
749
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
8 weeks ago • updated 7 weeks ago gene_bioconductor ▴ 10
1
vote
2
replies
310
views
Citation for edgeR user guide
edgeR
written 9 weeks ago by ▴ 30
4
votes
6
replies
599
views
FilterByExpr low counts with small sample size
edgeR
10 weeks ago • updated 9 weeks ago Jonathan ▴ 10
0
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2
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204
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
10 weeks ago prity6459 • 0
0
votes
3
replies
278
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 10 weeks ago by 51k • written 10 weeks ago by • 0
5
votes
3
replies
416
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 weeks ago by 51k • written 10 weeks ago by • 0
3
votes
3
replies
439
views
permutation test in edgeR
rna-seq edgeR
updated 10 weeks ago by 51k • written 12 weeks ago by • 0
1
vote
3
replies
436
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 11 weeks ago by 51k • written 11 weeks ago by • 0
5
votes
6
replies
549
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 11 weeks ago by ★ 4.2k • written 11 weeks ago by ▴ 50
1
vote
3
replies
332
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 12 weeks ago by 66k • written 12 weeks ago by • 0
0
votes
2
replies
265
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
12 weeks ago Marianna ▴ 20
0
votes
4
replies
515
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
3 months ago Lucy ▴ 60
3
votes
5
replies
527
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 3 months ago by 51k • written 3 months ago by • 0
0
votes
6
replies
459
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 3 months ago by 51k • written 3 months ago by • 0
0
votes
1
reply
311
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 3 months ago by 51k • written 3 months ago by • 0
5
votes
3
replies
862
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 3 months ago by 51k • written 3 months ago by ▴ 50
2
votes
3
replies
367
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 3 months ago by 51k • written 3 months ago by • 0
0
votes
2
replies
355
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 3 months ago by 51k • written 3 months ago by • 0
2
votes
2
replies
333
views
between lane normalization upper quantile
EDASeq edgeR
3 months ago elesofi • 0
2
votes
2
replies
336
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
3 months ago Sabiha ▴ 20
1
vote
3
replies
506
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 5 months ago by • 0
0
votes
1
reply
275
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 3 months ago by 51k • written 3 months ago by • 0
0
votes
11
replies
897
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 3 months ago by 51k • written 4 months ago by • 0
0
votes
1
reply
340
views
ExactTest vs QLFTest
edgeR
updated 4 months ago by 51k • written 4 months ago by • 0
1
vote
6
replies
606
views
Library size normalization in methylation count analysis
edgeR MethylationArray
4 months ago mico • 0
2
votes
6
replies
512
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
4 months ago tsl0026 • 0
5
votes
4
replies
492
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
4 months ago pl23 • 0
0
votes
8
replies
787
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
4 months ago Marianna ▴ 20
3
votes
2
replies
616
views
How does one test for interactions in EdgeR?
edgeR
4 months ago pl23 • 0
0
votes
4
replies
435
views
Nested paired design
edgeR
4 months ago manduchi ▴ 10
1
vote
2
replies
421
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
4 months ago mico • 0
2
votes
3
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445
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 4 months ago by 66k • written 4 months ago by • 0
4
votes
4
replies
497
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 5 months ago by 66k • written 5 months ago by • 0
6
votes
7
replies
676
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 5 months ago by 51k • written 5 months ago by • 0
1
vote
8
replies
667
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 5 months ago by 51k • written 5 months ago by • 0
0
votes
0
replies
322
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
5 months ago Jawahar • 0
2
votes
4
replies
858
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
5 months ago Sabiha ▴ 20
0
votes
3
replies
568
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 5 months ago by 51k • written 5 months ago by • 0
3
votes
3
replies
853
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 5 months ago by 51k • written 5 months ago by • 0
4
votes
9
replies
1.2k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
5 months ago Luca • 0
0
votes
1
reply
351
views
download problem
edgeR
updated 5 months ago by 51k • written 5 months ago by • 0
0
votes
5
replies
710
views
Help with model for differential expression analysis
DifferentialExpression edgeR
6 months ago • updated 5 months ago Lucy ▴ 60
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Thank you for your support. > In the double conversion, the output you supplied indicates that the number of probes is the same (453093)? …
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One can also check out a professional solution named Weeom OST to PST Converter Software. It is a reliable and secure solution to repair co…
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Thank you very much for your detailed reply, this was a big help. Just in case others come across this problem in the future, the code did …
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C: ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Help with error running DiffBind
Comment: Difference between enrichGO results and Enrichr website results
A: Unable to install the package "tissuesGeneExpression"
Unable to install the package "tissuesGeneExpression"
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