Showing : edgeR • reset
4
votes
2
replies
345
views
When to use edgeR or limma
edgeR limma
updated 20 days ago by 53k • written 23 days ago by • 0
3
votes
4
replies
331
views
Question about the filterByExpr function inputs in edgeR
RNASeq filter design edgeR model.matrix
23 days ago • updated 22 days ago mohammedtoufiq91 ▴ 10
8
votes
8
replies
2.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
written 7.4 years ago by ▴ 20
0
votes
3
replies
343
views
How to do differential expresion across time serise with edgeR?
edgeR timecoursedata
updated 4 weeks ago by 53k • written 4 weeks ago by ▴ 10
0
votes
3
replies
328
views
segfault in edgeR glmQLFit
edgeR
updated 6 weeks ago by 53k • written 6 weeks ago by • 0
1
vote
2
replies
515
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 12 weeks ago by ★ 4.0k • written 4 months ago by • 0
0
votes
1
reply
271
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
2
votes
2
replies
382
views
replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 4 months ago by 53k • written 4 months ago by • 0
0
votes
4
replies
498
views
voomLmFit fitted log-CPM values
limma edgeR
updated 5 months ago by 53k • written 5 months ago by ▴ 10
2
votes
9
replies
1.1k
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
5 months ago mohammedtoufiq91 ▴ 10
3
votes
2
replies
1.1k
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
6 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.0k
views
Using offset in edgeR
edgeR
updated 6 months ago by 53k • written 6 months ago by • 0
4
votes
8
replies
2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
5
votes
11
replies
3.9k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 9 months ago by ▴ 10
2
votes
4
replies
2.8k
views
Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
8 months ago Maziya • 0
2
votes
3
replies
1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
0
votes
2
replies
973
views
edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 8 months ago by ▴ 110 • written 8 months ago by • 0
0
votes
3
replies
1.1k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 10 months ago by ▴ 10
10
votes
13
replies
3.1k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 9 months ago by 53k • written 9 months ago by ▴ 20
2
votes
2
replies
1.6k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
5
votes
3
replies
1.3k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 10 months ago by 53k • written 10 months ago by ▴ 10
2
votes
2
replies
1.7k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
11 months ago • updated 10 months ago Elizabeth • 0
0
votes
2
replies
846
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 months ago by 43k • written 11 months ago by ▴ 20
0
votes
1
reply
506
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 11 months ago by 53k • written 11 months ago by • 0
0
votes
4
replies
1.5k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 11 months ago by • 0 • written 11 months ago by • 0
2
votes
4
replies
1.1k
views
EdgeR Biological CVs
edgeR
written 12 months ago by • 0
3
votes
5
replies
2.4k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 12 months ago by 68k • written 12 months ago by ▴ 10
0
votes
2
replies
834
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
13 months ago gingergeiger22 • 0
0
votes
1
reply
680
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
1
vote
8
replies
1.7k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
13 months ago Andre • 0
1
vote
9
replies
1.7k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 13 months ago by ▴ 40
6
votes
10
replies
3.8k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 14 months ago by ★ 5.0k • written 14 months ago by ▴ 10
7
votes
6
replies
1.5k
views
ANOVA like approach of edgeR
edgeR
updated 14 months ago by 53k • written 14 months ago by ▴ 10
3
votes
3
replies
1.0k
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
2
votes
4
replies
2.8k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 15 months ago by 53k • written 15 months ago by • 0
1
vote
8
replies
2.8k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 15 months ago by • 0
0
votes
1
reply
951
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 15 months ago by 68k • written 15 months ago by • 0
3
votes
3
replies
1.7k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 15 months ago by • 0
0
votes
4
replies
1.2k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
15 months ago Philippine • 0
4
votes
6
replies
2.0k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
15 months ago altintas.ali • 0
1
vote
2
replies
787
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
15 months ago Hongjian • 0
3
votes
3
replies
847
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
16 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
754
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 16 months ago by 53k • written 16 months ago by • 0
1
vote
1
reply
762
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
1
vote
2
replies
971
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 16 months ago by 43k • written 16 months ago by ▴ 10
0
votes
2
replies
888
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 16 months ago by 53k • written 16 months ago by • 0
1
vote
2
replies
769
views
Inconsistent result in edgeR
edgeR
16 months ago hiroko.ohmiya • 0
1
vote
1
reply
960
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 17 months ago by 53k • written 17 months ago by • 0
2
votes
9
replies
1.7k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 17 months ago by 53k • written 17 months ago by • 0
2,035 results • Page 1 of 41
Recent ...
Replies
Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Votes
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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