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Showing :
Tximport
•
reset
0
votes
2
replies
166
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
4 weeks ago
Marianna
▴ 20
0
votes
2
replies
206
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
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
0
votes
1
reply
347
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
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
3
votes
2
replies
561
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
3
replies
427
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
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
4
votes
13
replies
1.4k
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
0
votes
4
replies
879
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
807
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 8 months ago by
Vitor
• 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
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
Ndimensional
▴ 20
0
votes
2
replies
663
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
1
reply
610
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
655
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 11 months ago by
Michael Love
41k • written 11 months ago by
prangannathofficial
• 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
12 months ago
Yijing
• 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 14 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
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
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
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
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
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
0
votes
5
replies
9.3k
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
24 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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