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0
votes
3
answers
107
views
3
answers
How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2 salmon tximport written 8 days ago by bruno.saubamea • 0
0
votes
1
answer
245
views
1
answer
confusion with tximport options and resulting matrix
rnaseq limma voom tximport rsem written 23 days ago by arubio • 0 • updated 23 days ago by Gordon Smyth ♦ 31k
1
vote
1
answer
87
views
1
answer
tximport error with salmon version
deseq2 salmon tximport written 4 weeks ago by agetzler • 0 • updated 4 weeks ago by Michael Love ♦ 13k
1
vote
1
answer
88
views
1
answer
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
R bioconductor salmon tximport written 5 weeks ago by macmanes • 0 • updated 5 weeks ago by Michael Love ♦ 13k
0
votes
1
answer
73
views
1
answer
how to deal with the cufflinks files
tximport written 6 weeks ago by xiaoaozqd • 0 • updated 6 weeks ago by Michael Love ♦ 13k
1
vote
1
answer
100
views
1
answer
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport written 6 weeks ago by stan • 0 • updated 6 weeks ago by Michael Love ♦ 13k
0
votes
1
answer
122
views
1
answer
Different results obtained from mroast and camera from Deseq2 counts
limma camera mroast tximport written 7 weeks ago by jarod_v6@libero.it • 20 • updated 7 weeks ago by James W. MacDonald ♦ 44k
1
vote
0
answers
151
views
0
answers
How to test or estimate differential TSS/promoter usage/expression based on RNA-seq data only
rna-seq salmon tss tximport differential isoform usage written 7 weeks ago by Steffen Heyne • 10
0
votes
1
answer
219
views
1
answer
DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport written 9 weeks ago by bh129 • 0 • updated 9 weeks ago by Michael Love ♦ 13k
2
votes
1
answer
174
views
1
answer
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq normalization deseq2 salmon tximport written 9 weeks ago by kofoed • 0 • updated 9 weeks ago by Michael Love ♦ 13k
2
votes
1
answer
134
views
1
answer
tximport error: TXNAME from Txdb.mm10 and kallisto target_id mismatch
tximport kallisto txdb.mmusculus.ucsc.mm10.knowngene written 10 weeks ago by Kaustav • 0 • updated 10 weeks ago by James W. MacDonald ♦ 44k
0
votes
1
answer
145
views
1
answer
(very) conflicting results with DESeq2 between versions
rnaseq deseq2 R tximport kallisto written 10 weeks ago by birgittenilsson • 0 • updated 10 weeks ago by Michael Love ♦ 13k
0
votes
2
answers
386
views
2
answers
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
deseq2 salmon tximport "tximport" written 10 weeks ago by sunil.mangalam • 0
1
vote
1
answer
121
views
1
answer
tximport using for data generated from other tools
salmon tximport express written 10 weeks ago by saumya.kumar • 0 • updated 10 weeks ago by Michael Love ♦ 13k
0
votes
1
answer
189
views
1
answer
Error reading kallisto files using tximport for cross species RNA-Seq analysis
rna-seq tximport kallisto across species written 11 weeks ago by urjaswita • 0 • updated 11 weeks ago by Michael Love ♦ 13k
2
votes
1
answer
156
views
1
answer
check splice isoforms
deseq2 tximport written 3 months ago by ry82722 • 0 • updated 3 months ago by Michael Love ♦ 13k
1
vote
1
answer
354
views
1
answer
unable to get tximport to work on data from kallisto
tximport kallisto written 3 months ago by swamyvinny • 0 • updated 3 months ago by Steve Lianoglou ♦ 12k
3
votes
1
answer
516
views
1
answer
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport written 3 months ago by JWCarlson • 50
1
vote
1
answer
246
views
1
answer
RNA-seq analysis on mouse data with human contamination in controls
limma rna-seq salmon tximport written 3 months ago by Endre Sebestyen • 60 • updated 3 months ago by Aaron Lun • 15k
2
votes
1
answer
469
views
1
answer
Is there any point to TMM-normalize TPM prior to limma-voom?
edger voom tximport limma-voom written 4 months ago by johnmcma • 0 • updated 4 months ago by Ryan C. Thompson ♦ 5.9k
0
votes
1
answer
268
views
1
answer
tximport error reading salmon quantification files...
salmon tximport written 5 months ago by nschurch • 10 • updated 5 months ago by James W. MacDonald ♦ 44k
0
votes
1
answer
237
views
1
answer
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv written 5 months ago by seb.boegel • 0 • updated 5 months ago by Michael Love ♦ 13k
2
votes
1
answer
243
views
1
answer
txImport: a gene seems missing from the sample data
tximport tximportdata written 5 months ago by alexlok • 0 • updated 5 months ago by Michael Love ♦ 13k
3
votes
1
answer
306
views
1
answer
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
rnaseq cqn deseq2 salmon tximport written 5 months ago by dmr210 • 0 • updated 5 months ago by Michael Love ♦ 13k
8
votes
2
answers
968
views
2
answers
Using 'tximport' library for downstream DGE after quantifying with Kallisto
rna-seq tximport kallisto written 16 months ago by cguzman.bioinformatics • 10 • updated 5 months ago by pablo_garcia05 • 0
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