Showing : edger • reset
2
votes
3
replies
105
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 1 day ago by 50k • written 2 days ago by • 0
1
vote
2
replies
201
views
Citation for edgeR user guide
edgeR
written 23 days ago by ▴ 30
1
vote
3
replies
220
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 2 days ago by 50k • written 3 days ago by • 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 29 days ago by • 0
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
14 days ago • updated 10 days ago gene_bioconductor ▴ 10
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 14 days ago by 50k • written 14 days ago by • 0
4
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6
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464
views
FilterByExpr low counts with small sample size
edgeR
29 days ago • updated 24 days ago Jonathan ▴ 10
3
votes
3
replies
366
views
permutation test in edgeR
rna-seq edgeR
updated 26 days ago by 50k • written 5 weeks ago by • 0
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 28 days ago by • 0 • written 15 months ago by ▴ 10
0
votes
3
replies
208
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 28 days ago by 50k • written 28 days ago by • 0
0
votes
2
replies
146
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
28 days ago prity6459 • 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 28 days ago by • 0 • written 8.9 years ago by ▴ 30
1
vote
3
replies
368
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
votes
6
replies
456
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
1
vote
3
replies
278
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
0
votes
2
replies
195
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
votes
4
replies
447
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago Lucy ▴ 60
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 6 weeks ago by 50k • written 11.5 years ago by ▴ 30
3
votes
5
replies
412
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 6 weeks ago by 50k • written 12.5 years ago by ▴ 670
0
votes
6
replies
370
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
5
votes
3
replies
734
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
0
votes
1
reply
250
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
3
replies
309
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
2
replies
273
views
between lane normalization upper quantile
EDASeq edgeR
9 weeks ago • updated 8 weeks ago elesofi • 0
0
votes
2
replies
303
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
2
votes
2
replies
288
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
1
vote
3
replies
437
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
votes
4
replies
502
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
0
votes
11
replies
777
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
1
reply
238
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
0
votes
1
reply
279
views
ExactTest vs QLFTest
edgeR
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
1
vote
6
replies
525
views
Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago mico • 0
5
votes
4
replies
425
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
0
votes
8
replies
678
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 12 weeks ago Marianna ▴ 20
2
votes
6
replies
436
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago • updated 12 weeks ago tsl0026 • 0
3
votes
2
replies
493
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
1
vote
2
replies
347
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
0
votes
4
replies
364
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
2
votes
3
replies
386
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
3
votes
4
replies
8.7k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
1
vote
8
replies
571
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
4
votes
4
replies
455
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 4 months ago by • 0
0
votes
5
replies
641
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
6
votes
7
replies
599
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
0
replies
266
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
2
votes
4
replies
644
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
votes
3
replies
378
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
3
replies
709
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by 50k • written 4 months ago by • 0
50 results • Page 1 of 1
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Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning by angelaesper43 • 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
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Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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