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4
votes
1
answer
206
views
1
answer
Do I have batch effect?
rna-seq edger batch effect written 23 days ago by avino • 10 • updated 22 days ago by i.sudbery ♦ 8.1k
0
votes
1
answer
92
views
1
answer
nearestTSS function in edgeR for differential methylation analysis
rrbs nearesttss limma rna-seq edger written 24 days ago by osa.zuta • 0
4
votes
2
answers
172
views
2
answers
Why 'filterByExpr' does not eliminate low read counts from the expression data?
filterbyexpr degs edger rna-seq written 6 weeks ago by svp • 100 • updated 6 weeks ago by Gordon Smyth • 1.7k
1
vote
1
answer
96
views
1
answer
How to add dots to the PCA (in addition to labels)?
rna-seq edger written 7 weeks ago by tanya_fiskur • 30 • updated 7 weeks ago by Kevin Blighe ♦ 61k
0
votes
1
answer
197
views
1
answer
RNAseq analysis with edgeR-interaction terms and comparison within and between groups
rna-seq edger written 3 months ago by erwagner2 • 0 • updated 7 weeks ago by RamRS ♦ 27k
0
votes
1
answer
126
views
1
answer
DESeq2/RNA-Seq: Cross-study comparisons with large control-variance?
deseq2 rna-seq edger limma written 8 weeks ago by Felix • 0 • updated 7 weeks ago by Kevin Blighe ♦ 61k
2
votes
1
answer
209
views
1
answer
How to get differential gene expression within paired samples using EdgeR or DESeq2?
paired samples deseq2 designmatrix rna-seq edger written 7 weeks ago by learner.bioinformatics • 0
0
votes
1
answer
1.9k
views
1
answer
edgeR not available for Mavericks and R 3.1
software error R rna-seq edger written 6.2 years ago by Ann • 2.3k • updated 8 weeks ago by Biostar ♦♦ 20
3
votes
0
answers
220
views
0
answers
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
complexheatmap rna-seq clustering edger heatmap written 9 weeks ago by eggrandio • 40
4
votes
1
answer
192
views
1
answer
DEG analysis between 2 samples using edger
edger rna-seq biological_replicates written 10 weeks ago by bioyas • 0 • updated 9 weeks ago by Gordon Smyth • 1.7k
2
votes
1
answer
279
views
1
answer
Problem with differential analysis between two groups having low raw counts
differential analysis expression rna-seq edger written 10 weeks ago by Biologist • 190 • updated 10 weeks ago by ATpoint ♦ 36k
7
votes
1
answer
186
views
1
answer
Forum: DEG analysis when not replicates are available
replicates forum noiseq rna-seq edger written 10 weeks ago by Antonio R. Franco • 4.5k
2
votes
1
answer
138
views
1
answer
tximport --> edgeR
tximport edger rna-seq written 10 weeks ago by u3005992 • 0
0
votes
0
answers
200
views
0
answers
Help with Salmon --> tximport --> edgeR
tximport salmon rna-seq edger normalisation written 10 weeks ago by u3005992 • 0
0
votes
0
answers
118
views
0
answers
Differential expression analysis after RUVseq in Galaxy
galaxy limma-voom ruvseq rna-seq edger written 11 weeks ago by tanya_fiskur • 30
2
votes
1
answer
124
views
1
answer
Which DE method perform better for small number of genes
noiseq deseq2 ttest edger rna-seq written 11 weeks ago by thind.amarinder • 20 • updated 11 weeks ago by Devon Ryan ♦ 95k
3
votes
1
answer
268
views
1
answer
edger and continuous variables
rna-seq edger written 12 weeks ago by Do it! • 10 • updated 12 weeks ago by genomax ♦ 85k
1
vote
1
answer
228
views
1
answer
Filtering the genes based on cpm in edgeR
rna-seq edger written 12 weeks ago by elb • 170
3
votes
1
answer
188
views
1
answer
which normalization method for my RNA-seq data set?
deseq2 tpm rna-seq edger tmm written 3 months ago by nyoegut • 10 • updated 3 months ago by genomax ♦ 85k
0
votes
0
answers
92
views
0
answers
Experimental design with DOE and multi-factorial RNA-seq
doe additive models blocking rna-seq edger written 3 months ago by michelelole • 0
0
votes
1
answer
198
views
1
answer
Choosing between edgeR's exactTest and QLFTest for 2x2 design
edger rna-seq written 3 months ago by adam.faranda • 80
2
votes
2
answers
127
views
2
answers
How to set group in EdgeR and DEseq2?
R deseq2 rna-seq edger written 3 months ago by deb0612 • 10 • updated 3 months ago by nilislam3 • 0
2
votes
1
answer
2.8k
views
1
answer
Up/Down regulated genes list in EdgeR
diffrential gene expression rna-seq edger written 13 months ago by ali.hakimzadeh • 0 • updated 3 months ago by dr.camelia.quek • 0
3
votes
1
answer
1.4k
views
1
answer
RNA Seq: Differential expression model formula
R deseq rna-seq edger written 4.0 years ago by rmf • 940 • updated 3 months ago by Biostar ♦♦ 20
4
votes
1
answer
498
views
1
answer
Ensemble of Gene Set Enrichment Analyses (EGSEA) for count matrix generated by DESeq2 and edgeR packages
egsea deseq2 rna-seq gsea edger written 10 months ago by F. Golestan • 60 • updated 4 months ago by Biostar ♦♦ 20
18
votes
2
answers
372
views
7 follow
2
answers
Doing differential gene expression without knowing sample classes
deseq2 rna-seq edger written 11 months ago by A • 3.8k
0
votes
0
answers
141
views
0
answers
How to analyze DEGs other than makeContrasts method for time-point RNASeq experiment?
degs rna-seq edger written 4 months ago by anikng • 0
0
votes
0
answers
208
views
0
answers
'NA's under Gene Names & Gene Symbols : Differential expression Analysis of TCGA data using edgeR
gene tcga differential expression edger written 4 months ago by fawazfebin • 100
1
vote
1
answer
187
views
1
answer
RNA-seq differential analysis with N batches and a technical replicate in each batch
differential analysis deseq2 rna-seq edger written 4 months ago by jonathanli6022 • 0 • updated 4 months ago by Gordon Smyth • 1.7k
1
vote
0
answers
238
views
0
answers
RNA-Seq Time series analysis in EdgeR
R rna-seq edger written 4 months ago by josmantorres • 10
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