Showing : EDGER • reset
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14
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
13 hours ago ilaria.massaiu • 0
0
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0
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27
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
2 days ago Joseph • 0
0
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2
replies
128
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replace cat with message in glmTreat when lfc = 0
edgeR glmTreat
updated 13 days ago by 53k • written 17 days ago by • 0
0
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4
replies
275
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voomLmFit fitted log-CPM values
limma edgeR
updated 26 days ago by 53k • written 27 days ago by ▴ 10
2
votes
9
replies
743
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Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
7 weeks ago mohammedtoufiq91 ▴ 10
3
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2
replies
796
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
10 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
872
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Using offset in edgeR
edgeR
updated 10 weeks ago by 53k • written 11 weeks ago by • 0
4
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8
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1.8k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
11 weeks ago richardallenfriedmanbrooklyn ▴ 30
7
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9
replies
5.4k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
11 weeks ago bbao ▴ 10
5
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11
replies
3.0k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 5 months ago by ▴ 10
2
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4
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2.5k
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Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
4 months ago Maziya • 0
2
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3
replies
1.3k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
4 months ago Paulito • 0
0
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2
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815
views
edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 4 months ago by ▴ 110 • written 4 months ago by • 0
0
votes
3
replies
914
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 5 months ago by ▴ 10
10
votes
13
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2.3k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 5 months ago by 53k • written 5 months ago by ▴ 20
2
votes
2
replies
1.4k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 6 months ago by ★ 4.9k • written 6 months ago by • 0
5
votes
3
replies
1.1k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 6 months ago by 53k • written 6 months ago by ▴ 10
2
votes
2
replies
1.5k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
6 months ago Elizabeth • 0
0
votes
2
replies
680
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 6 months ago by 43k • written 6 months ago by ▴ 20
0
votes
1
reply
404
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 7 months ago by 53k • written 7 months ago by • 0
0
votes
4
replies
1.4k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 7 months ago by • 0 • written 7 months ago by • 0
2
votes
4
replies
847
views
EdgeR Biological CVs
edgeR
written 8 months ago by • 0
3
votes
5
replies
1.8k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 8 months ago by 68k • written 8 months ago by ▴ 10
0
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2
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611
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
9 months ago • updated 8 months ago gingergeiger22 • 0
0
votes
1
reply
566
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
1
vote
8
replies
1.5k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
9 months ago • updated 8 months ago Andre • 0
1
vote
9
replies
1.4k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 9 months ago by ▴ 30
6
votes
10
replies
3.3k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 9 months ago by ★ 4.9k • written 10 months ago by ▴ 10
7
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6
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1.3k
views
ANOVA like approach of edgeR
edgeR
updated 10 months ago by 53k • written 10 months ago by ▴ 10
3
votes
3
replies
865
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 10 months ago by 53k • written 10 months ago by • 0
2
votes
4
replies
2.4k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 10 months ago by 53k • written 10 months ago by • 0
1
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8
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2.4k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 months ago by • 0
0
votes
1
reply
845
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 11 months ago by 68k • written 11 months ago by • 0
3
votes
3
replies
1.5k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 11 months ago by • 0
0
votes
4
replies
993
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
11 months ago Philippine • 0
4
votes
6
replies
1.7k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
11 months ago altintas.ali • 0
1
vote
2
replies
663
views
edgeR 4.2.2 not compiled for Windows
edger edgeR
11 months ago Hongjian • 0
3
votes
3
replies
684
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
11 months ago Guido Hooiveld ★ 4.1k
4
votes
1
reply
615
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 11 months ago by 53k • written 11 months ago by • 0
1
vote
1
reply
532
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 12 months ago by ★ 4.9k • written 12 months ago by • 0
1
vote
2
replies
824
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 12 months ago by 43k • written 12 months ago by ▴ 10
0
votes
2
replies
740
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 12 months ago by 53k • written 12 months ago by • 0
1
vote
2
replies
654
views
Inconsistent result in edgeR
edgeR
12 months ago hiroko.ohmiya • 0
1
vote
1
reply
806
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 13 months ago by 53k • written 13 months ago by • 0
2
votes
9
replies
1.4k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 13 months ago by 53k • written 13 months ago by • 0
0
votes
3
replies
964
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 13 months ago by • 0
2
votes
1
reply
2.0k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 13 months ago by ★ 29k • written 14 months ago by • 0
0
votes
1
reply
718
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 13 months ago by 53k • written 14 months ago by • 0
3
votes
3
replies
1000
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 14 months ago by 68k • written 14 months ago by ▴ 60
0
votes
4
replies
1.0k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 14 months ago by • 0
2,031 results • Page 1 of 41
Recent ...
Replies
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
Comment: Sharing a collection of datasets in ExperimentHub by Peter Hickey ▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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