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txImportData
•
reset
0
votes
4
replies
543
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
5 months ago
JG13
• 0
2
votes
9
replies
1.7k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
16 months ago
Ndimensional
▴ 20
0
votes
2
replies
891
views
tximport error in reading salmon output files?
tximport
tximportData
updated 9 months ago by
Matteo
• 0 • written 16 months ago by
barrypraveen
• 0
2
votes
3
replies
1.6k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
23 months ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
1.3k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
2.0 years ago
duhwa.lee
• 0
0
votes
4
replies
1.4k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
2.4 years ago
uhlkatie
• 0
2
votes
3
replies
1.2k
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 2.7 years ago by
Michael Love
42k • written 2.7 years ago by
Luisa
• 0
0
votes
3
replies
1.1k
views
tximport fails when RSEM output options produce files with additional columns?
DESeq2
tximportData
tximpor
updated 3.3 years ago by
Michael Love
42k • written 3.3 years ago by
Alexander
• 0
0
votes
1
reply
989
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 3.5 years ago by
Michael Love
42k • written 3.5 years ago by
pthom010
• 0
0
votes
7
replies
2.0k
views
Problem with Tximport
tximportData
tximport
3.8 years ago
agoesmartini
• 0
0
votes
1
reply
1.1k
views
How to use tx import on output of abundance file
tximportData
tximport
updated 4.0 years ago by
Kevin Blighe
★ 4.0k • written 4.0 years ago by
Julie
• 0
0
votes
4
replies
1.4k
views
Having a hard time creating a Txi object from an existing Salmon output file to convert transcript file to gene id TPM
Salmon
tximport
tximportdata
ensembl
updated 4.6 years ago by
Michael Love
42k • written 4.6 years ago by
slouis
• 0
1
vote
2
replies
1.2k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
6.0 years ago
fcuy047
• 0
1
vote
2
replies
1.3k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
Stanley Yang
• 0
1
vote
8
replies
35k
views
How to create tx2gene.gencode.v27.csv
tximportdata
updated 6.4 years ago by
Michael Love
42k • written 6.4 years ago by
mmokrejs
• 0
2
votes
6
replies
1.8k
views
[DESeq2] Different results from tutorial
deseq2
tximportdata
tximport
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
changhan1110
• 0
0
votes
1
reply
2.6k
views
could not find function "tximport"
tximportdata
updated 6.7 years ago by
Gordon Smyth
51k • written 6.7 years ago by
s.corley
▴ 30
0
votes
9
replies
3.7k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 6.8 years ago by
hauken_heyken
▴ 80 • written 8.4 years ago by
jarod_v6@libero.it
▴ 40
0
votes
3
replies
14k
views
Problem installing tximportData
tximportdata
7.7 years ago
elg
• 0
3
votes
5
replies
2.9k
views
txImport: a gene seems missing from the sample data
txImportData
txImport
updated 3.8 years ago by
James W. MacDonald
67k • written 7.7 years ago by
alexlok
• 0
0
votes
1
reply
1.8k
views
How to remove genes with 0 counts in tximport?
tximport
deseq
tximportdata
deseq2
updated 7.7 years ago by
Michael Love
42k • written 7.7 years ago by
Peter Alto
▴ 10
0
votes
7
replies
1.9k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 8.3 years ago by
Michael Love
42k • written 8.3 years ago by
jarod_v6@libero.it
▴ 40
22 results • Page
1 of 1
Recent ...
Replies
Comment: Question about using LRT test for time course experiments with DESeq2
by
James W. MacDonald
67k
You don't want to add a logFC on top like that, as it invalidates the p-value. Maybe I wasn't clear before. The LRT gives you all the gene…
Comment: Question about using LRT test for time course experiments with DESeq2
by
Denise
• 0
Hi James, Thank you very much for your very detailed explanation! I guess my question is simpler than that, I just want to union, across…
Answer: featureCounts segmentation fault with large chromosomes
by
vkkodali
▴ 10
Thanks to @yangliao this issue is fixed in subread v2.0.8
Comment: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
by
ATpoint
★ 4.5k
For the general audience, reticulate / python (which basilisk depends on / wraps) requires explicit declaration of integers, so one needs i…
Answer: Average expression of genes across replicates
by
ATpoint
★ 4.5k
Not sure what you're asking. The average expression across all samples is what the `baseMean` column of `results()` returns. This is simply…
Votes
Answer: featureCounts segmentation fault with large chromosomes
Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
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abadgerw
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Mike Smith
★ 6.6k
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Guido Hooiveld
★ 4.1k
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Gordon Smyth
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