Showing : edgeR • reset
2
votes
9
replies
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
934
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 18 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
1.4k
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
694
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
772
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 22 months ago by ▴ 70
1
vote
3
replies
993
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
939
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
940
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
605
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
756
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
Recent ...
Replies
Answer: bcftools norm Equivalent by a2a2hd42aa • 0
it lacks a direct, single function equivalent to bcftools norm for variant normalization. Bioinformaticians often bridge this gap by using …
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.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
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
Awards • All
Popular Question to Jaqueline • 0
Scholar to Gordon Smyth 53k
Popular Question to Dario Strbenac ★ 1.6k
Popular Question to chirag.parsania ▴ 10
Popular Question to Michael Love 43k
Locations • All
WEHI, Melbourne, Australia, 1 hour ago
The city by the bay, 4 hours ago
United States, 5 hours ago
Pakistan, 9 hours ago
United States, 9 hours ago
Traffic: 1833 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6