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tximportdata
•
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2
votes
9
replies
1.1k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
9 months ago
Ndimensional
▴ 20
0
votes
2
replies
631
views
tximport error in reading salmon output files?
tximport
tximportData
updated 10 weeks ago by
Matteo
• 0 • written 10 months ago by
barrypraveen
• 0
2
votes
3
replies
1.2k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
16 months ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
896
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
18 months ago • updated 17 months ago
duhwa.lee
• 0
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
21 months ago
uhlkatie
• 0
2
votes
3
replies
938
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
Luisa
• 0
0
votes
3
replies
901
views
tximport fails when RSEM output options produce files with additional columns?
DESeq2
tximportData
tximpor
updated 2.8 years ago by
Michael Love
41k • written 2.8 years ago by
Alexander
• 0
0
votes
1
reply
832
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
pthom010
• 0
0
votes
7
replies
1.7k
views
Problem with Tximport
tximportData
tximport
3.2 years ago
agoesmartini
• 0
0
votes
1
reply
908
views
How to use tx import on output of abundance file
tximportData
tximport
updated 3.4 years ago by
Kevin Blighe
★ 3.9k • written 3.4 years ago by
Julie
• 0
0
votes
4
replies
1.1k
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 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
slouis
• 0
1
vote
2
replies
1.0k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
5.5 years ago
fcuy047
• 0
1
vote
2
replies
1.2k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
Stanley Yang
• 0
1
vote
8
replies
33k
views
How to create tx2gene.gencode.v27.csv
tximportdata
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
mmokrejs
• 0
2
votes
6
replies
1.6k
views
[DESeq2] Different results from tutorial
deseq2
tximportdata
tximport
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
changhan1110
• 0
0
votes
1
reply
2.3k
views
could not find function "tximport"
tximportdata
updated 6.1 years ago by
Gordon Smyth
50k • written 6.1 years ago by
s.corley
▴ 30
0
votes
9
replies
3.5k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 6.2 years ago by
hauken_heyken
▴ 80 • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
0
votes
3
replies
13k
views
Problem installing tximportData
tximportdata
7.1 years ago
elg
• 0
3
votes
5
replies
2.7k
views
txImport: a gene seems missing from the sample data
txImportData
txImport
updated 3.2 years ago by
James W. MacDonald
65k • written 7.1 years ago by
alexlok
• 0
0
votes
1
reply
1.7k
views
How to remove genes with 0 counts in tximport?
tximport
deseq
tximportdata
deseq2
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
Peter Alto
▴ 10
0
votes
7
replies
1.7k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
21 results • Page
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Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it always helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR? Are you starting with…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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