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0
votes
1
answer
42
views
1
answer
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon written 1 day ago by LD • 0 • updated 1 day ago by Michael Love ♦ 17k
0
votes
1
answer
152
views
1
answer
Using tximport on rsem files produces error while trying to read in files
rnaseq R tpm tximport rsem written 7 weeks ago by stephan.emmrich • 0
2
votes
1
answer
92
views
1
answer
tximport failing at importing TPM instead of FPKM
rnaseq tximport rsem written 12 weeks ago by fresard.laure • 0 • updated 12 weeks ago by rosabellascottgm • 0
2
votes
2
answers
179
views
2
answers
tximport's parameter for countsFromAbundance doesn't work
edger tximport rsem written 3 months ago by tim.ivanov.92 • 0
0
votes
1
answer
137
views
1
answer
Data object format for deseq2
deseq2 R rsem written 4 months ago by tim.ivanov.92 • 0 • updated 4 months ago by Michael Love ♦ 17k
1
vote
1
answer
276
views
1
answer
RNA-seq read alignment best practices for low-input samples
alignment limma differential gene expression rsem rnaseq analysis written 5 months ago by goldberg.jm • 0 • updated 5 months ago by Aaron Lun • 19k
1
vote
1
answer
235
views
1
answer
Importing RSEM transcript-level data using tximport
tximport rsem written 5 months ago by Patrick Kimes • 0 • updated 5 months ago by Michael Love ♦ 17k
0
votes
1
answer
233
views
1
answer
Tximport with RSEM error
rsem written 7 months ago by hs.lansdell • 10 • updated 7 months ago by k.vitting.seerup • 20
2
votes
1
answer
220
views
1
answer
Obtaining transcript names in RSEM
tximport rsem written 8 months ago by deena • 10 • updated 8 months ago by Michael Love ♦ 17k
0
votes
1
answer
312
views
1
answer
Using RSEM reads for DESeq2
deseq2 rsem written 8 months ago by deeptiptl74 • 0 • updated 8 months ago by Michael Love ♦ 17k
3
votes
1
answer
478
views
1
answer
Filtering step in Differential analysis with RSEM values
edger differential gene expression rsem written 9 months ago by Biologist • 60 • updated 9 months ago by Gordon Smyth ♦ 33k
0
votes
1
answer
671
views
1
answer
confusion with tximport options and resulting matrix
rnaseq limma voom tximport rsem written 10 months ago by arubio • 0 • updated 10 months ago by Gordon Smyth ♦ 33k
1
vote
1
answer
295
views
1
answer
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem written 10 months ago by Biologist • 60 • updated 10 months ago by James W. MacDonald ♦ 46k
5
votes
1
answer
628
views
1
answer
Clustering differential expression results from voomWithQualityWeights
limma edger rna rsem written 13 months ago by hrishi27n • 0 • updated 13 months ago by Gordon Smyth ♦ 33k
0
votes
0
answers
681
views
0
answers
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
rnaseq normalization R tcga rsem written 14 months ago by panagiotis.mokos • 10
0
votes
1
answer
461
views
1
answer
RSEM output in DeSeq2
deseq2 count matrix rsem written 15 months ago by kmeusemann • 0 • updated 15 months ago by Michael Love ♦ 17k
24
votes
3
answers
1.8k
views
9 follow
3
answers
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq normalization edger tcga rsem written 16 months ago by svlachavas • 570 • updated 16 months ago by Gordon Smyth ♦ 33k
0
votes
1
answer
2.0k
views
1
answer
Expected counts from RSEM in DESeq2
deseq2 rsem expected_counts raw_counts written 16 months ago by chudar.chudar • 0 • updated 16 months ago by Michael Love ♦ 17k
5
votes
2
answers
1.5k
views
2
answers
Voom: need at least two non-NA values to interpolate
voom fpkm limma voom rsem written 20 months ago by komal.rathi • 40
0
votes
3
answers
540
views
3
answers
Using Scran with RSEM/DEseq
normalization edger deseq2 scran rsem written 21 months ago by a.guerra • 0
6
votes
2
answers
799
views
2
answers
RSEM expected counts to limma-voom
limma voom rsem written 22 months ago by Jake • 60 • updated 22 months ago by Gordon Smyth ♦ 33k
4
votes
1
answer
429
views
1
answer
assigning differential exons to trascripts
dexseq differential gene expression differential exon usage rsem written 23 months ago by Assa Yeroslaviz • 1.4k • updated 23 months ago by James W. MacDonald ♦ 46k
1
vote
2
answers
759
views
2
answers
DESeq2 size factors estimation after RSEM quantification
deseq2 estimatesizefactors tximport rsem written 2.0 years ago by Hugo Varet • 80
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