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edgeR
•
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0
votes
3
replies
1.2k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2
edgeR
DifferentialExpression
written 17 months ago by
dancingcow
• 0
2
votes
1
reply
2.6k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData
Clustering
memory
SingleCellExperiment
edgeR
updated 17 months ago by
Aaron Lun
★ 29k • written 17 months ago by
Joseph
• 0
0
votes
1
reply
869
views
edgeR - design a complex matrix
design
model.matrix
edgeR
complexdesign
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Karla
• 0
3
votes
3
replies
1.2k
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Ahdee
▴ 60
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 18 months ago by
Shaozhen
• 0
1
vote
8
replies
2.0k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 18 months ago by
Gordon Smyth
53k • written 19 months ago by
Alec
• 0
3
votes
5
replies
3.8k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 19 months ago by
Reza Ghamsari
• 0 • written 23 months ago by
Jack S.
▴ 60
0
votes
4
replies
1.3k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression
scran
scater
SingleCellExperiment
edgeR
19 months ago
vohara4
• 0
3
votes
6
replies
1.4k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
19 months ago
JG13
• 0
3
votes
2
replies
1.3k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
20 months ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
1.3k
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Guillermo
• 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 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Ashley
• 0
0
votes
1
reply
687
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
z_bahari
• 0
4
votes
2
replies
1.9k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
21 months ago • updated 20 months ago
gene_bioconductor
▴ 10
1
vote
2
replies
1.9k
views
Citation for edgeR user guide
edgeR
written 21 months ago by
k___
▴ 30
4
votes
6
replies
2.0k
views
FilterByExpr low counts with small sample size
edgeR
21 months ago
Jonathan
▴ 10
0
votes
2
replies
756
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
21 months ago
prity6459
• 0
0
votes
3
replies
1.1k
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
prity6459
• 0
5
votes
3
replies
1.7k
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 20 months ago by
Gordon Smyth
53k • written 21 months ago by
Shaimaa Gamal
• 0
3
votes
3
replies
1.9k
views
permutation test in edgeR
rna-seq
edgeR
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Netanel
• 0
1
vote
3
replies
1.0k
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Simran
• 0
5
votes
6
replies
1.6k
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
nhaus
▴ 70
1
vote
3
replies
974
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Shaimaa Gamal
• 0
0
votes
2
replies
1.0k
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
22 months ago
Marianna
▴ 20
0
votes
4
replies
1.6k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
22 months ago
Lucy
▴ 60
3
votes
6
replies
2.5k
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
written 22 months ago by
Fabian
• 0
0
votes
6
replies
1.4k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 22 months ago by
Gordon Smyth
53k • written 22 months ago by
Faisal
• 0
0
votes
1
reply
1.2k
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 22 months ago by
Gordon Smyth
53k • written 22 months ago by
scoops_streams_06
• 0
8
votes
5
replies
3.7k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 15 months ago by
Gordon Smyth
53k • written 22 months ago by
Jack S.
▴ 60
2
votes
3
replies
1.1k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 22 months ago by
Gordon Smyth
53k • written 22 months ago by
JKim
• 0
0
votes
2
replies
923
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 22 months ago by
Gordon Smyth
53k • written 22 months ago by
z_bahari
• 0
2
votes
2
replies
1.0k
views
between lane normalization upper quantile
EDASeq
edgeR
22 months ago
elesofi
• 0
2
votes
2
replies
912
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
22 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 24 months ago by
pl23
• 0
0
votes
1
reply
589
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 23 months ago by
Gordon Smyth
53k • written 23 months ago by
Fabian
• 0
0
votes
11
replies
2.0k
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 23 months ago by
Gordon Smyth
53k • written 23 months ago by
mico
• 0
0
votes
1
reply
739
views
ExactTest vs QLFTest
edgeR
updated 23 months ago by
Gordon Smyth
53k • written 23 months ago by
fr8712ca-s
• 0
1
vote
7
replies
1.9k
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
updated 15 months ago by
juansmurphy
• 0 • written 23 months ago by
mico
• 0
2
votes
6
replies
1.1k
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
23 months ago
tsl0026
• 0
5
votes
4
replies
1.2k
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
23 months ago
pl23
• 0
0
votes
8
replies
1.9k
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
23 months ago
Marianna
▴ 20
5
votes
2
replies
2.0k
views
How does one test for interactions in EdgeR?
edgeR
23 months ago
pl23
• 0
0
votes
4
replies
989
views
Nested paired design
edgeR
23 months ago
manduchi
▴ 10
1
vote
2
replies
1.2k
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
23 months ago
mico
• 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Shaimaa Gamal
• 0
4
votes
4
replies
1.0k
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 24 months ago by
James W. MacDonald
68k • written 2.0 years ago by
Geo
• 0
6
votes
7
replies
1.3k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 24 months ago by
Gordon Smyth
53k • written 24 months ago by
aa.machado001
• 0
1
vote
8
replies
1.6k
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 24 months ago by
Gordon Smyth
53k • written 2.0 years ago by
sat
• 0
0
votes
0
replies
1.0k
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
2.0 years ago
Jawahar
• 0
2
votes
4
replies
2.7k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
2.0 years ago
Sabiha
▴ 20
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