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1
vote
1
answer
49
views
1
answer
trouble importing data for DEseq2 workflow
deseq2 tutorial pasilla tximport tximportdata written 8 days ago by Stanley Yang • 0 • updated 8 days ago by Michael Love ♦ 19k
2
votes
2
answers
72
views
2
answers
tximport and de novo transcriptome
tximport salmon rna seq de novo written 21 days ago by RMRG • 10 • updated 20 days ago by James W. MacDonald ♦ 48k
1
vote
2
answers
57
views
2
answers
Help with error produced when using makeTxDbFromBiomart
tximport tximport rnaseq written 5 weeks ago by pat20 • 0 • updated 5 weeks ago by James W. MacDonald ♦ 48k
2
votes
2
answers
161
views
2
answers
Get the countsFromAbundance as limma input
limma deseq2 differential expression tximport written 6 weeks ago by Darklings • 0 • updated 6 weeks ago by Gordon Smyth ♦ 35k
1
vote
1
answer
98
views
1
answer
tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
bos taurus ensembldb tximport tx2gene written 11 weeks ago by gilles.charpigny • 0 • updated 11 weeks ago by James W. MacDonald ♦ 48k
0
votes
1
answer
107
views
1
answer
DESeq2/tximport 'duplicate rownames not allowed' error
deseq2 tximport written 11 weeks ago by ctl • 0
0
votes
1
answer
167
views
1
answer
tximport allfile.exists(files)--> FALSE
tximport written 12 weeks ago by gilles.charpigny • 0 • updated 12 weeks ago by James W. MacDonald ♦ 48k
0
votes
1
answer
86
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1
answer
tximport latest version on bioconductor and bioconda
tximport written 3 months ago by sebio • 0 • updated 3 months ago by James W. MacDonald ♦ 48k
0
votes
1
answer
56
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1
answer
Tximport Input file
tximport written 3 months ago by akhilkrishnavs • 0 • updated 3 months ago by Michael Love ♦ 19k
0
votes
1
answer
75
views
1
answer
Using tximport on RSEM abundance date
rnaseq tximport rsem written 3 months ago by raeganlynn123 • 0 • updated 3 months ago by Michael Love ♦ 19k
1
vote
1
answer
113
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 3 months ago by al-ash • 20 • updated 3 months ago by Michael Love ♦ 19k
0
votes
1
answer
100
views
1
answer
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem written 3 months ago by celi0001 • 0 • updated 3 months ago by Michael Love ♦ 19k
2
votes
2
answers
163
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2
answers
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
rnaseq edger salmon tximport written 4 months ago by martin.weihrauch • 10 • updated 4 months ago by Aaron Lun • 21k
2
votes
2
answers
170
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2
answers
[DESeq2] Different results from tutorial
deseq2 tximport tximportdata written 4 months ago by changhan1110 • 0 • updated 4 months ago by Michael Love ♦ 19k
0
votes
1
answer
249
views
1
answer
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon written 4 months ago by LD • 0 • updated 4 months ago by Michael Love ♦ 19k
0
votes
1
answer
160
views
1
answer
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
salmon ensembldb tximport written 5 months ago by user31888 • 30 • updated 5 months ago by Johannes Rainer • 1.3k
2
votes
2
answers
271
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2
answers
how to get the lastest version of tximport
stringtie tximport written 7 months ago by matrs • 0
1
vote
1
answer
693
views
1
answer
tximport using for data generated from other tools
salmon tximport express written 16 months ago by saumya.kumar • 0 • updated 5 months ago by Michael Love ♦ 19k
0
votes
1
answer
263
views
1
answer
there is no "tx2gene.gencode.v27.csv" in tximportData
tximport written 5 months ago by krwyaong.ju • 0 • updated 5 months ago by Michael Love ♦ 19k
0
votes
1
answer
212
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1
answer
Tutorial: Importing multiple .h5 files using tximport
tutorial tximport written 5 months ago by nelson.s.garcia • 0 • updated 5 months ago by Steve Lianoglou ♦ 12k
1
vote
1
answer
161
views
1
answer
Post-processing RNA-Seq after tximport
deseq2 tximport salmon rna seq ruv-seq written 5 months ago by mad6kj • 0 • updated 5 months ago by Michael Love ♦ 19k
18
votes
2
answers
3.9k
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 2.3 years ago by tangming2005 • 90 • updated 5 months ago by luxeredias • 10
1
vote
1
answer
198
views
1
answer
processing of (salmon) gene counts for eqtl analysis
tmm salmon gene length tximport eqtl written 5 months ago by VSM • 120 • updated 5 months ago by Michael Love ♦ 19k
1
vote
1
answer
184
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 6 months ago by pvd2107 • 0
0
votes
1
answer
360
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1
answer
Using tximport on rsem files produces error while trying to read in files
rnaseq R tpm tximport rsem written 6 months ago by stephan.emmrich • 0
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