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Showing :
txImport
•
reset
10
votes
9
replies
164
views
tximport error: vroom
tximport
16 hours ago • updated 1 hour ago
RLiu
▴ 40
4
votes
13
replies
538
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 7 days ago by
Michael Love
40k • written 5 weeks ago by
Christian
• 0
2
votes
3
replies
338
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 7 weeks ago by
Vitor
• 0
0
votes
4
replies
311
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 5 weeks ago by
Michael Love
40k • written 6 weeks ago by
hanc
• 0
1
vote
2
replies
288
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 9 weeks ago by
k.vitting.seerup
▴ 120 • written 9 weeks ago by
elva.gypsophila
▴ 10
14
votes
25
replies
2.2k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 4.5 years ago by
fiona.dick91
▴ 60
1
vote
5
replies
2.2k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 11 weeks ago by
Michael Love
40k • written 23 months ago by
nicolette.sipperly
• 0
2
votes
9
replies
632
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
3 months ago • updated 12 weeks ago
Ndimensional
▴ 20
0
votes
2
replies
312
views
tximport error in reading salmon output files?
tximport
tximportData
3 months ago
barrypraveen
• 0
4
votes
9
replies
3.9k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 4 months ago by
IUH
• 0 • written 6.3 years ago by
stan
• 0
0
votes
4
replies
942
views
tximport importer isoform abundance
tximport
updated 4 months ago by
tangming2005
▴ 190 • written 3.3 years ago by
Ina Hoeschele
▴ 620
0
votes
1
reply
313
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 4 months ago by
James W. MacDonald
63k • written 4 months ago by
Yijing
• 0
2
votes
1
reply
316
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 4 months ago by
Michael Love
40k • written 4 months ago by
prangannathofficial
• 0
3
votes
7
replies
593
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
5 months ago • updated 4 months ago
Yijing
• 0
0
votes
2
replies
372
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
5 months ago
Yijing
• 0
1
vote
3
replies
422
views
tximport error
tximport
r
updated 5 months ago by
Michael Love
40k • written 5 months ago by
Joana
• 0
0
votes
2
replies
438
views
combining multiple salmon runs after tximport
tximport
RNASeq
salmon
updated 7 months ago by
ATpoint
★ 3.4k • written 7 months ago by
Ivana
• 0
1
vote
5
replies
666
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 7 months ago by
Michael Love
40k • written 7 months ago by
Michael Steinbaugh
▴ 90
3
votes
5
replies
781
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
7 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
405
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 8 months ago by
Dario Strbenac
★ 1.5k • written 8 months ago by
Hicham
▴ 10
0
votes
2
replies
493
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 8 months ago by
camilia.savitri
• 0
0
votes
1
reply
402
views
Missing transcript
DESeq2
tximport
salmon
updated 9 months ago by
ATpoint
★ 3.4k • written 9 months ago by
camilia.savitri
• 0
2
votes
1
reply
404
views
Confused about tximport-DESeq2 setup
DESeq2
tximport
salmon
updated 9 months ago by
ATpoint
★ 3.4k • written 9 months ago by
Dunois
• 0
2
votes
2
replies
657
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
written 9 months ago by
kiqbal
• 0
0
votes
2
replies
480
views
Differentially expression analysis of orthologous genes between two species
DESeq2
tximport
10 months ago
Konstantinos
• 0
2
votes
3
replies
765
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
10 months ago
mohammedtoufiq91
▴ 10
4
votes
3
replies
638
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene
tximport
Arabidopsis_thaliana
kallisto
updated 10 months ago by
James W. MacDonald
63k • written 10 months ago by
Mikhail Biryukov
▴ 10
0
votes
4
replies
1.6k
views
Tximport error message - colnames
tximport
written 2.3 years ago by
bryce.thomas
• 0
0
votes
1
reply
549
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 10 months ago by
ATpoint
★ 3.4k • written 10 months ago by
Jenni
• 0
1
vote
2
replies
497
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
11 months ago • updated 10 months ago
cta
• 0
3
votes
3
replies
571
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
11 months ago
duhwa.lee
• 0
2
votes
2
replies
765
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
11 months ago
L
▴ 50
32 results • Page
1 of 1
Recent ...
Replies
Comment: tximport error: vroom
by
RLiu
▴ 40
yes! worked perfectly! Thank you~
Comment: tximport error: vroom
by
Benji Bromberg
▴ 20
Worked perfectly! Thanks!
Comment: tximport error: vroom
by
Michael Love
40k
You can force the function used for importing: https://github.com/thelovelab/tximport/blob/devel/R/tximport.R#L265 Try `importer=read.del…
Comment: tximport error: vroom
by
Benji Bromberg
▴ 20
Of course! Let me know if you figure it out.
Comment: tximport error: vroom
by
RLiu
▴ 40
Thank you for providing this clue. I never installed vroom manually. I guess it is one of dependences for tximport that automatically insta…
Votes
Comment: tximport error: vroom
Comment: tximport error: vroom
Comment: tximport error: vroom
Comment: tximport error: vroom
Comment: tximport error: vroom
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