Showing : edger • reset
2
votes
9
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1.8k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 18 months ago by 53k • written 18 months ago by • 0
0
votes
3
replies
1.3k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 18 months ago by • 0
2
votes
1
reply
3.0k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 18 months ago by ★ 29k • written 18 months ago by • 0
0
votes
1
reply
939
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 18 months ago by 53k • written 18 months ago by • 0
3
votes
3
replies
1.3k
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 19 months ago by 68k • written 19 months ago by ▴ 60
0
votes
4
replies
1.2k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 19 months ago by • 0
1
vote
8
replies
2.2k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 19 months ago by 53k • written 20 months ago by • 0
3
votes
5
replies
4.4k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 20 months ago by • 0 • written 24 months ago by ▴ 60
0
votes
4
replies
1.4k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
20 months ago vohara4 • 0
3
votes
6
replies
1.5k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
21 months ago JG13 • 0
3
votes
2
replies
1.4k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
21 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
1.3k
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
1
vote
3
replies
1.2k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
1
reply
696
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
4
votes
2
replies
2.0k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
22 months ago gene_bioconductor ▴ 10
1
vote
2
replies
2.2k
views
Citation for edgeR user guide
edgeR
written 22 months ago by ▴ 30
4
votes
6
replies
2.3k
views
FilterByExpr low counts with small sample size
edgeR
22 months ago Jonathan ▴ 10
0
votes
2
replies
773
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
22 months ago prity6459 • 0
0
votes
3
replies
1.1k
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 22 months ago by 53k • written 22 months ago by • 0
5
votes
3
replies
1.8k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 21 months ago by 53k • written 22 months ago by • 0
3
votes
3
replies
2.1k
views
permutation test in edgeR
rna-seq edgeR
updated 22 months ago by 53k • written 23 months ago by • 0
1
vote
3
replies
1.0k
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 22 months ago by 53k • written 22 months ago by • 0
5
votes
6
replies
1.7k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 22 months ago by ★ 5.0k • written 23 months ago by ▴ 70
1
vote
3
replies
994
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 23 months ago by 68k • written 23 months ago by • 0
0
votes
2
replies
1.1k
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
23 months ago Marianna ▴ 20
0
votes
4
replies
1.7k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
23 months ago Lucy ▴ 60
3
votes
6
replies
2.6k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 23 months ago by • 0
0
votes
6
replies
1.4k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 23 months ago by 53k • written 23 months ago by • 0
0
votes
1
reply
1.3k
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 23 months ago by 53k • written 23 months ago by • 0
8
votes
5
replies
4.0k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 16 months ago by 53k • written 23 months ago by ▴ 60
2
votes
3
replies
1.2k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 23 months ago by 53k • written 23 months ago by • 0
0
votes
2
replies
941
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 0
2
votes
2
replies
1.0k
views
between lane normalization upper quantile
EDASeq edgeR
23 months ago elesofi • 0
2
votes
2
replies
941
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
23 months ago Sabiha ▴ 20
1
vote
3
replies
1.1k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 2.1 years ago by • 0
0
votes
1
reply
606
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 24 months ago by 53k • written 24 months ago by • 0
0
votes
11
replies
2.1k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 24 months ago by 53k • written 2.0 years ago by • 0
0
votes
1
reply
757
views
ExactTest vs QLFTest
edgeR
updated 24 months ago by 53k • written 2.0 years ago by • 0
1
vote
7
replies
1.9k
views
Library size normalization in methylation count analysis
edgeR MethylationArray
updated 16 months ago by • 0 • written 2.0 years ago by • 0
2
votes
6
replies
1.1k
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
2.0 years ago tsl0026 • 0
5
votes
4
replies
1.2k
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
2.0 years ago pl23 • 0
0
votes
8
replies
2.0k
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
2.0 years ago Marianna ▴ 20
5
votes
2
replies
2.1k
views
How does one test for interactions in EdgeR?
edgeR
2.1 years ago • updated 2.0 years ago pl23 • 0
0
votes
4
replies
1.0k
views
Nested paired design
edgeR
2.1 years ago manduchi ▴ 10
1
vote
2
replies
1.3k
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
2.1 years ago mico • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
4
votes
4
replies
1.0k
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
6
votes
7
replies
1.3k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
1
vote
8
replies
1.8k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
votes
0
replies
1.1k
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
2.1 years ago Jawahar • 0
2,036 results • Page 2 of 41
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Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
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SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
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Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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