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Tximport
•
reset
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 7 months ago by
Michael Love
41k • written 8 months ago by
Christian
• 0
10
votes
11
replies
1.9k
views
tximport error: vroom
tximport
updated 6 months ago by
Abhishek
• 0 • written 7 months ago by
RLiu
▴ 40
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 13 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
10 months ago • updated 9 months ago
Ndimensional
▴ 20
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 11 months ago by
IUH
• 0 • written 6.8 years ago by
stan
• 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
12 months ago • updated 11 months ago
Yijing
• 0
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 6 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
1
vote
5
replies
2.8k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 9 months ago by
Michael Love
41k • written 2.5 years ago by
nicolette.sipperly
• 0
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 10 weeks ago by
Michael Love
41k • written 16 months ago by
kiqbal
• 0
0
votes
4
replies
1.2k
views
tximport importer isoform abundance
tximport
updated 11 months ago by
tangming2005
▴ 190 • written 3.9 years ago by
Ina Hoeschele
▴ 620
0
votes
4
replies
876
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 8 months ago by
Michael Love
41k • written 8 months ago by
hanc
• 0
2
votes
3
replies
804
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 8 months ago by
Vitor
• 0
2
votes
3
replies
1.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.3k • written 4 months ago by
Bo
• 0
0
votes
3
replies
425
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon
tximport
deseq2
updated 6 months ago by
Michael Love
41k • written 6 months ago by
Kayleigh
• 0
0
votes
2
replies
157
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
29 days ago
Marianna
▴ 20
0
votes
2
replies
662
views
tximport error in reading salmon output files?
tximport
tximportData
updated 3 months ago by
Matteo
• 0 • written 10 months ago by
barrypraveen
• 0
0
votes
2
replies
205
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
SG
• 0
1
vote
2
replies
1.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 9 months ago by
k.vitting.seerup
▴ 120 • written 9 months ago by
elva.gypsophila
▴ 10
3
votes
2
replies
559
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
mckinlee.salazar
• 0
0
votes
1
reply
344
views
tximport error with rsem files
rsem
tximport
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
apolitics
• 0
2
votes
1
reply
650
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 11 months ago by
Michael Love
41k • written 11 months ago by
prangannathofficial
• 0
0
votes
1
reply
608
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Yijing
• 0
2
votes
1
reply
246
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 7 weeks ago by
ATpoint
★ 4.1k • written 7 weeks ago by
hemantcnaik
• 0
24 results • Page
1 of 1
Recent ...
Replies
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
James W. MacDonald
65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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