Search
2
votes
2
answers
54
views
2
answers
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
rnaseq edger salmon tximport written 9 hours ago by martin.weihrauch • 10 • updated 9 hours ago by Aaron Lun • 19k
2
votes
2
answers
69
views
2
answers
[DESeq2] Different results from tutorial
deseq2 tximport tximportdata written 2 days ago by changhan1110 • 0 • updated 2 days ago by Michael Love ♦ 17k
0
votes
1
answer
48
views
1
answer
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon written 4 days ago by LD • 0 • updated 4 days ago by Michael Love ♦ 17k
0
votes
1
answer
52
views
1
answer
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
salmon ensembldb tximport written 7 days ago by user31888 • 30 • updated 6 days ago by Johannes Rainer • 1.3k
2
votes
2
answers
156
views
2
answers
how to get the lastest version of tximport
stringtie tximport written 12 weeks ago by matrs • 0
1
vote
1
answer
437
views
1
answer
tximport using for data generated from other tools
salmon tximport express written 11 months ago by saumya.kumar • 0 • updated 15 days ago by Michael Love ♦ 17k
0
votes
1
answer
40
views
1
answer
there is no "tx2gene.gencode.v27.csv" in tximportData
tximport written 15 days ago by krwyaong.ju • 0 • updated 15 days ago by Michael Love ♦ 17k
0
votes
1
answer
68
views
1
answer
Tutorial: Importing multiple .h5 files using tximport
tutorial tximport written 17 days ago by nelson.s.garcia • 0 • updated 17 days ago by Steve Lianoglou ♦ 12k
1
vote
1
answer
58
views
1
answer
Post-processing RNA-Seq after tximport
deseq2 tximport salmon rna seq ruv-seq written 23 days ago by mad6kj • 0 • updated 23 days ago by Michael Love ♦ 17k
18
votes
2
answers
2.7k
views
6 follow
2
answers
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
rnaseq deseq2 rpkm tpm tximport written 22 months ago by tangming2005 • 90 • updated 28 days ago by luxeredias • 10
1
vote
1
answer
88
views
1
answer
processing of (salmon) gene counts for eqtl analysis
tmm salmon gene length tximport eqtl written 4 weeks ago by VSM • 120 • updated 29 days ago by Michael Love ♦ 17k
1
vote
1
answer
112
views
1
answer
Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (Removing Genes without symbols)
deseq2 org.mm.eg.db gencode tximport written 8 weeks ago by pvd2107 • 0
0
votes
1
answer
154
views
1
answer
Using tximport on rsem files produces error while trying to read in files
rnaseq R tpm tximport rsem written 8 weeks ago by stephan.emmrich • 0
0
votes
1
answer
114
views
1
answer
Collapsing transcript counts into pathways / gene lists with DESeq2
deseq2 pathway analysis tximport written 9 weeks ago by Gon Nido • 0 • updated 9 weeks ago by Michael Love ♦ 17k
0
votes
1
answer
84
views
1
answer
filtering lowly expressed genes before or after normalization?
edger tximport written 9 weeks ago by burcu.atasu • 0 • updated 9 weeks ago by Michael Love ♦ 17k
1
vote
1
answer
148
views
1
answer
Can Tximport average transcript length be used for GOSeq?
goseq deseq2 tximport written 9 weeks ago by casey.rimland • 70
1
vote
1
answer
98
views
1
answer
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
rnaseq deseq2 tximport kallisto written 10 weeks ago by Yunlu Zhu • 0 • updated 10 weeks ago by Michael Love ♦ 17k
0
votes
1
answer
68
views
1
answer
tximport error with Salmon in DESeq2 pipeline
deseq2 salmon tximport written 10 weeks ago by seyfim • 0 • updated 10 weeks ago by Michael Love ♦ 17k
0
votes
1
answer
107
views
1
answer
Subsetting a tximport object
tximport written 11 weeks ago by scanchi • 0 • updated 11 weeks ago by jennietodd141 • 0
0
votes
1
answer
93
views
1
answer
use tximport's countsFromAbundance when using DESeq2
rnaseq normalization deseq2 salmon tximport written 11 weeks ago by ginlucks • 0 • updated 11 weeks ago by Michael Love ♦ 17k
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
3
votes
1
answer
293
views
1
answer
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
salmon tximport michael love tx2gene written 3 months ago by pvd2107 • 0 • updated 3 months ago by Michael Love ♦ 17k
0
votes
1
answer
98
views
1
answer
Support site search not finding posts?
search tximport limma-trend written 3 months ago by Jenny Drnevich • 1.9k • updated 3 months ago by James W. MacDonald ♦ 46k
4
votes
1
answer
185
views
1
answer
Trouble with Tximport for edgeR
edger tximport written 3 months ago by Xiang Wang • 0 • updated 3 months ago by Gordon Smyth ♦ 33k
2
votes
2
answers
180
views
2
answers
tximport's parameter for countsFromAbundance doesn't work
edger tximport rsem written 3 months ago by tim.ivanov.92 • 0
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