Showing : edger • reset
1
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8
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1.8k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 16 months ago by 53k • written 16 months ago by • 0
3
votes
5
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3.3k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 16 months ago by • 0 • written 20 months ago by ▴ 60
0
votes
4
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1.2k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
17 months ago vohara4 • 0
3
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6
replies
1.3k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
17 months ago JG13 • 0
3
votes
2
replies
1.2k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
17 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
1.2k
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
1
vote
3
replies
1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 18 months ago by 53k • written 18 months ago by • 0
0
votes
1
reply
635
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
4
votes
2
replies
1.8k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
18 months ago gene_bioconductor ▴ 10
1
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2
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1.6k
views
Citation for edgeR user guide
edgeR
written 18 months ago by ▴ 30
4
votes
6
replies
1.8k
views
FilterByExpr low counts with small sample size
edgeR
19 months ago • updated 18 months ago Jonathan ▴ 10
0
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2
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700
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
19 months ago prity6459 • 0
0
votes
3
replies
969
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 19 months ago by 53k • written 19 months ago by • 0
5
votes
3
replies
1.5k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 months ago by 53k • written 19 months ago by • 0
3
votes
3
replies
1.8k
views
permutation test in edgeR
rna-seq edgeR
updated 18 months ago by 53k • written 19 months ago by • 0
1
vote
3
replies
948
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 19 months ago by 53k • written 19 months ago by • 0
5
votes
6
replies
1.5k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 19 months ago by ★ 5.0k • written 19 months ago by ▴ 70
1
vote
3
replies
894
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
2
replies
915
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
19 months ago Marianna ▴ 20
0
votes
4
replies
1.5k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
19 months ago Lucy ▴ 60
3
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6
replies
2.2k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 19 months ago by • 0
0
votes
6
replies
1.3k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 19 months ago by 53k • written 19 months ago by • 0
0
votes
1
reply
1.1k
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 19 months ago by 53k • written 20 months ago by • 0
8
votes
5
replies
3.2k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 12 months ago by 53k • written 20 months ago by ▴ 60
2
votes
3
replies
1.1k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
2
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854
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 20 months ago by 53k • written 20 months ago by • 0
2
votes
2
replies
938
views
between lane normalization upper quantile
EDASeq edgeR
20 months ago elesofi • 0
2
votes
2
replies
835
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
20 months ago Sabiha ▴ 20
1
vote
3
replies
1.0k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 21 months ago by • 0
0
votes
1
reply
549
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
11
replies
1.9k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
1
reply
702
views
ExactTest vs QLFTest
edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
1
vote
7
replies
1.7k
views
Library size normalization in methylation count analysis
edgeR MethylationArray
updated 12 months ago by • 0 • written 20 months ago by • 0
2
votes
6
replies
1.0k
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
21 months ago tsl0026 • 0
5
votes
4
replies
1.1k
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
21 months ago • updated 20 months ago pl23 • 0
0
votes
8
replies
1.8k
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
21 months ago Marianna ▴ 20
5
votes
2
replies
1.8k
views
How does one test for interactions in EdgeR?
edgeR
21 months ago pl23 • 0
0
votes
4
replies
883
views
Nested paired design
edgeR
21 months ago manduchi ▴ 10
1
vote
2
replies
1.1k
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
21 months ago mico • 0
2
votes
3
replies
1.1k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 21 months ago by 68k • written 21 months ago by • 0
4
votes
4
replies
929
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 21 months ago by 68k • written 22 months ago by • 0
6
votes
7
replies
1.2k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
1
vote
8
replies
1.5k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
0
replies
926
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
22 months ago Jawahar • 0
2
votes
4
replies
2.1k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
22 months ago Sabiha ▴ 20
0
votes
3
replies
1.3k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
3
votes
3
replies
1.9k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
4
votes
9
replies
2.4k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
22 months ago Luca • 0
0
votes
1
reply
617
views
download problem
edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
0
votes
5
replies
1.4k
views
Help with model for differential expression analysis
DifferentialExpression edgeR
22 months ago • updated 21 months ago Lucy ▴ 60
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Comment: Research and Service Group Leader positions in AI in Biology at EMBL by eja.gssssswssswwse.r.m • 0
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
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Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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