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1
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1
answer
52
views
1
answer
tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
bos taurus ensembldb tximport tx2gene written 14 days ago by gilles.charpigny • 0 • updated 13 days ago by James W. MacDonald ♦ 47k
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1
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45
views
1
answer
DESeq2/tximport 'duplicate rownames not allowed' error
deseq2 tximport written 13 days ago by ctl • 0
0
votes
1
answer
68
views
1
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tximport allfile.exists(files)--> FALSE
tximport written 20 days ago by gilles.charpigny • 0 • updated 20 days ago by James W. MacDonald ♦ 47k
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1
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46
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1
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tximport latest version on bioconductor and bioconda
tximport written 26 days ago by sebio • 0 • updated 26 days ago by James W. MacDonald ♦ 47k
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votes
1
answer
34
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1
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Tximport Input file
tximport written 29 days ago by akhilkrishnavs • 0 • updated 29 days ago by Michael Love ♦ 19k
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votes
1
answer
46
views
1
answer
Using tximport on RSEM abundance date
rnaseq tximport rsem written 5 weeks ago by raeganlynn123 • 0 • updated 5 weeks ago by Michael Love ♦ 19k
1
vote
1
answer
74
views
1
answer
DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 differential expression tximport rsem sequence length normalization written 7 weeks ago by al-ash • 10 • updated 7 weeks ago by Michael Love ♦ 19k
0
votes
1
answer
64
views
1
answer
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem written 7 weeks ago by celi0001 • 0 • updated 7 weeks ago by Michael Love ♦ 19k
2
votes
2
answers
127
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2
answers
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
rnaseq edger salmon tximport written 11 weeks ago by martin.weihrauch • 10 • updated 11 weeks ago by Aaron Lun • 20k
2
votes
2
answers
132
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2
answers
[DESeq2] Different results from tutorial
deseq2 tximport tximportdata written 11 weeks ago by changhan1110 • 0 • updated 11 weeks ago by Michael Love ♦ 19k
0
votes
1
answer
178
views
1
answer
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon written 12 weeks ago by LD • 0 • updated 12 weeks ago by Michael Love ♦ 19k
0
votes
1
answer
117
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1
answer
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
salmon ensembldb tximport written 12 weeks ago by user31888 • 30 • updated 12 weeks ago by Johannes Rainer • 1.3k
2
votes
2
answers
227
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2
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how to get the lastest version of tximport
stringtie tximport written 5 months ago by matrs • 0
1
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1
answer
585
views
1
answer
tximport using for data generated from other tools
salmon tximport express written 14 months ago by saumya.kumar • 0 • updated 3 months ago by Michael Love ♦ 19k
0
votes
1
answer
158
views
1
answer
there is no "tx2gene.gencode.v27.csv" in tximportData
tximport written 3 months ago by krwyaong.ju • 0 • updated 3 months ago by Michael Love ♦ 19k
0
votes
1
answer
156
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1
answer
Tutorial: Importing multiple .h5 files using tximport
tutorial tximport written 3 months ago by nelson.s.garcia • 0 • updated 3 months ago by Steve Lianoglou ♦ 12k
1
vote
1
answer
118
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1
answer
Post-processing RNA-Seq after tximport
deseq2 tximport salmon rna seq ruv-seq written 3 months ago by mad6kj • 0 • updated 3 months ago by Michael Love ♦ 19k
18
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2
answers
3.3k
views
6 follow
2
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difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
rnaseq deseq2 rpkm tpm tximport written 2.1 years ago by tangming2005 • 90 • updated 3 months ago by luxeredias • 10
1
vote
1
answer
153
views
1
answer
processing of (salmon) gene counts for eqtl analysis
tmm salmon gene length tximport eqtl written 3 months ago by VSM • 120 • updated 3 months ago by Michael Love ♦ 19k
1
vote
1
answer
143
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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 4 months ago by pvd2107 • 0
0
votes
1
answer
243
views
1
answer
Using tximport on rsem files produces error while trying to read in files
rnaseq R tpm tximport rsem written 4 months ago by stephan.emmrich • 0
0
votes
1
answer
162
views
1
answer
Collapsing transcript counts into pathways / gene lists with DESeq2
deseq2 pathway analysis tximport written 4 months ago by Gon Nido • 0 • updated 4 months ago by Michael Love ♦ 19k
0
votes
1
answer
132
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1
answer
filtering lowly expressed genes before or after normalization?
edger tximport written 4 months ago by burcu.atasu • 0 • updated 4 months ago by Michael Love ♦ 19k
1
vote
1
answer
189
views
1
answer
Can Tximport average transcript length be used for GOSeq?
goseq deseq2 tximport written 4 months ago by casey.rimland • 100
1
vote
1
answer
151
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1
answer
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
rnaseq deseq2 tximport kallisto written 5 months ago by Yunlu Zhu • 0 • updated 5 months ago by Michael Love ♦ 19k
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