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4
votes
1
answer
76
views
1
answer
EdgeR: Explaning dispersion types to newbies
visualization edger estimatedispersions dispersion teaching written 2 days ago by Mr.RB • 10 • updated 2 days ago by Aaron Lun • 19k
3
votes
1
answer
70
views
1
answer
Does Fold change cutoff changes the FDR value using glmTreat function in edgeR?
edger R bioconductor fdr diffferential expression written 3 days ago by Biologist • 70 • updated 3 days ago by James W. MacDonald ♦ 46k
1
vote
1
answer
63
views
1
answer
edgeR: setting up proper contrasts for interactions
limma edger written 3 days ago by fcamus • 0 • updated 3 days ago by Aaron Lun • 19k
6
votes
2
answers
151
views
2
answers
Differentially expressed genes selection with FC and FDR cutoff
rnaseq edger R bioconductor written 6 days ago by Beginner • 0 • updated 4 days ago by Gordon Smyth ♦ 33k
1
vote
1
answer
51
views
1
answer
How to change sample names in featureCounts or edgeR
edger featurecounts written 7 days ago by Gary • 0 • updated 7 days ago by Gordon Smyth ♦ 33k
5
votes
2
answers
168
views
2
answers
How does edgeR cpm function calculate log(CPM) values?
edger cpm written 11 weeks ago by jxb.dev • 10 • updated 7 days ago by ftroot1010 • 0
1
vote
1
answer
65
views
1
answer
EdgeR - How to set up the design matrix for a multifactorial experimental design with interactions?
edger edger main and interaction effects glmfit written 10 days ago by DonnyB • 0 • updated 10 days ago by Aaron Lun • 19k
2
votes
1
answer
81
views
1
answer
How edgeR reads an R List object produced by featureCounts
edger featurecounts written 11 days ago by Gary • 0 • updated 11 days ago by Gordon Smyth ♦ 33k
1
vote
2
answers
88
views
2
answers
edgeR for continuous independent variables
edger written 16 days ago by ycding • 10 • updated 15 days ago by Gordon Smyth ♦ 33k
1
vote
1
answer
51
views
1
answer
post hoc analysis on nested model
edger nested design post hoc written 19 days ago by ashley.lu • 0 • updated 18 days ago by Aaron Lun • 19k
2
votes
1
answer
94
views
1
answer
Up/Down Regulated GeneList from edgeR and R
edger R genelist up reg written 20 days ago by drskm7 • 0 • updated 19 days ago by Gordon Smyth ♦ 33k
4
votes
2
answers
101
views
2
answers
scaling data for clustering heat map
rnaseq clustering edger differential gene expression heatmap written 24 days ago by Beginner • 0 • updated 23 days ago by Gordon Smyth ♦ 33k
6
votes
1
answer
92
views
1
answer
How to obtain a normalised expression matrix from read counts and scaling factors
edger written 29 days ago by user31888 • 30 • updated 29 days ago by Ryan C. Thompson ♦ 6.8k
2
votes
1
answer
65
views
1
answer
another contrast question - edgeR + scRNA-seq + timecourse
timecourse edger design and contrast matrix single cell written 29 days ago by regan.hayward • 0 • updated 29 days ago by Gordon Smyth ♦ 33k
5
votes
2
answers
151
views
2
answers
Why DESeq2 and edgeR give different results?
rnaseq edger deseq2 differential gene expression written 4 weeks ago by Biologist • 70 • updated 29 days ago by Gordon Smyth ♦ 33k
2
votes
2
answers
93
views
2
answers
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
rnaseq edger salmon tximport written 4 weeks ago by martin.weihrauch • 10 • updated 4 weeks ago by Aaron Lun • 19k
3
votes
1
answer
88
views
1
answer
Calling svaseq() multiple times
limma edger sva svaseq written 4 weeks ago by cats_dogs • 0 • updated 4 weeks ago by Ryan C. Thompson ♦ 6.8k
0
votes
0
answers
57
views
0
answers
processAmplicons to match sequences 1 or 2 bases shorter than guides?
edger processamplicons written 5 weeks ago by sdalin • 0 • updated 4 weeks ago by shepherl ♦♦ 620
4
votes
1
answer
111
views
1
answer
edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression design matrix model.matrix written 4 weeks ago by grabear • 0 • updated 4 weeks ago by Gordon Smyth ♦ 33k
0
votes
1
answer
311
views
1
answer
EdgeR: run processAmplicons without barcodes
edger processamplicons crispr barcode written 15 months ago by neggersjasper • 0 • updated 5 weeks ago by sdalin • 0
3
votes
2
answers
76
views
2
answers
single continuous factor
edger design matrix continuous written 5 weeks ago by ashley.lu • 0 • updated 5 weeks ago by Gordon Smyth ♦ 33k
5
votes
2
answers
185
views
2
answers
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
normalization edger variancestabilizingtransformation cpm rnaseq analysis written 6 weeks ago by svlachavas • 570 • updated 6 weeks ago by Wolfgang Huber ♦ 13k
2
votes
2
answers
78
views
2
answers
CQN and EdgeR Library Size for Normalization
normalization edger cqn atac-seq written 6 weeks ago by shankasal • 0
4
votes
2
answers
213
views
2
answers
Filtering step for differential analysis in edgeR
edger R bioconductor differential gene expression filtering written 6 weeks ago by Biologist • 70 • updated 6 weeks ago by Gordon Smyth ♦ 33k
0
votes
2
answers
131
views
2
answers
edgeR and DESeq2
edger deseq2 written 6 weeks ago by yueli7 • 0 • updated 6 weeks ago by Gordon Smyth ♦ 33k
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