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10
votes
1
answer
1.5k
views
5 follow
1
answer
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq limma edger deseq2 voom written 2.3 years ago by Sean Davis ♦ 20k • updated 3 days ago by Paul Harrison • 60
0
votes
1
answer
70
views
1
answer
DESeq2 biological replicates and RIN values
rnaseq deseq2 differential gene expression covariates written 5 days ago by pmoranlosada • 0 • updated 3 days ago by Michael Love ♦ 13k
0
votes
1
answer
40
views
1
answer
differentially expressed genes form RSEM genes data
rnaseq edger written 3 days ago by lily • 10 • updated 3 days ago by Gordon Smyth ♦ 31k
0
votes
1
answer
53
views
1
answer
RNA-Seq DEG analysis questions
rnaseq deg written 5 days ago by mullin.yu • 0 • updated 5 days ago by Gordon Smyth ♦ 31k
8
votes
1
answer
104
views
1
answer
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
rnaseq limma edger independent filtering written 10 days ago by Robert Castelo • 2.0k
0
votes
0
answers
82
views
0
answers
Combined strand specific and unstranded samples
rnaseq strand counts differential gene expression batch effect written 11 days ago by lirongrossmann • 0
2
votes
1
answer
114
views
1
answer
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 differential gene expression wald lrt written 13 days ago by chrysanthi.taxiarchi12 • 0 • updated 12 days ago by Gavin Kelly • 320
0
votes
1
answer
207
views
1
answer
Set rnaseq locial flag during GSVA
rnaseq gsva tpm written 6 weeks ago by leiendeckerlu • 0 • updated 20 days ago by Robert Castelo • 2.0k
0
votes
1
answer
199
views
1
answer
R script problem
rnaseq R bioconductor written 20 days ago by fernanro • 0 • updated 20 days ago by James W. MacDonald ♦ 44k
2
votes
0
answers
196
views
0
answers
Why does total unique map not equal to library size?
rnaseq star htseqcounts written 22 days ago by Ahdee • 30
0
votes
2
answers
323
views
2
answers
Regarding scRNA seq vs Bulk RNA seq
rnaseq single cell written 24 days ago by naman.sep • 0 • updated 24 days ago by galib36 • 10
1
vote
1
answer
332
views
1
answer
DESEq2 p-values weird distribution under the H0 and fdrtool
rnaseq deseq2 differential gene expression fdrtool written 4 weeks ago by thyagoleal • 20
0
votes
1
answer
310
views
1
answer
SGSeq: moving toward diffex from SGSeq analysis
rnaseq sgseq written 4 weeks ago by Sylvain Foisy • 20 • updated 4 weeks ago by Leonard Goldstein • 20
1
vote
1
answer
313
views
1
answer
High variation among biological replicates. Options for correction during DE analysis
rnaseq written 4 weeks ago by hac141 • 0 • updated 4 weeks ago by Aaron Lun • 16k
2
votes
2
answers
370
views
2
answers
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq limma geoquery edger rna-seq written 5 weeks ago by hkarakurt • 10 • updated 5 weeks ago by Sean Davis ♦ 20k
0
votes
0
answers
344
views
0
answers
Ballgown with replicates and the adjustvars option
rnaseq differential gene expression ballgown written 5 weeks ago by o.diogosilva • 0
0
votes
1
answer
151
views
1
answer
Time series comparison with DESEQ2
rnaseq deseq2 rna written 5 weeks ago by hrishi27n • 0 • updated 5 weeks ago by Michael Love ♦ 13k
4
votes
2
answers
451
views
2
answers
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq edger dge no replicates written 6 weeks ago by Stefany Solano • 0
4
votes
1
answer
423
views
1
answer
Testing for DE genes between samples of isolated cells, accounting for expression in whole tissue
rnaseq limma rna-seq multiple factor design model-matrix written 6 weeks ago by smurray • 10 • updated 6 weeks ago by Aaron Lun • 16k
0
votes
1
answer
391
views
1
answer
DESeq2 multifactorialdesign contrasts
rnaseq deseq2 design and contrast matrix multifactorial design written 6 weeks ago by reubenmcgregor88 • 0 • updated 6 weeks ago by Gavin Kelly • 320
4
votes
1
answer
508
views
7 follow
1
answer
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
rnaseq deseq2 design lrt reduced model written 4 months ago by I.Castanho • 20 • updated 6 weeks ago by maksims.fiosins • 0
7
votes
3
answers
276
views
3
answers
Estimating cell size factors for single cell RNA-seq data
rnaseq normalization deseq2 scrnaseq written 6 weeks ago by gquon • 10 • updated 6 weeks ago by Michael Love ♦ 13k
0
votes
1
answer
188
views
1
answer
Is the CPM filtering method from NOISeq unsupervised?
rnaseq noiseq gene filtering de analysis written 6 weeks ago by Mau • 0 • updated 6 weeks ago by James W. MacDonald ♦ 44k
1
vote
1
answer
392
views
1
answer
Read normalization in derfinder
rnaseq normalization derfinder written 6 weeks ago by helene.gylling • 0 • updated 6 weeks ago by Leonardo Collado Torres • 540
0
votes
0
answers
375
views
0
answers
Polyester - creating simulated reads based on raw count matrix
rnaseq polyester simulation written 6 weeks ago by sseo2 • 0
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