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tximportData
•
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0
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267
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Error: lexical error: invalid char in json text (alevin-seurat)
tximpo
tximportData
alevinQC
updated 3 months ago by
ATpoint
★ 4.8k • written 3 months ago by
ptlsugam
• 0
0
votes
1
reply
543
views
Need new version : tx2gene.gencode.v47.csv
tximportData
updated 5 months ago by
Guido Hooiveld
★ 4.1k • written 5 months ago by
Gaurav
• 0
4
votes
5
replies
1.1k
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
6 months ago
LuciaNhu
• 0
0
votes
4
replies
775
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
11 months ago
JG13
• 0
2
votes
9
replies
2.0k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
23 months ago • updated 22 months ago
Ndimensional
▴ 20
0
votes
2
replies
1.1k
views
tximport error in reading salmon output files?
tximport
tximportData
updated 15 months ago by
Matteo
• 0 • written 23 months ago by
barrypraveen
• 0
2
votes
3
replies
1.9k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
2.5 years ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
1.6k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
2.6 years ago • updated 2.5 years ago
duhwa.lee
• 0
0
votes
4
replies
1.7k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
2.9 years ago
uhlkatie
• 0
2
votes
3
replies
1.3k
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
Luisa
• 0
0
votes
3
replies
1.3k
views
tximport fails when RSEM output options produce files with additional columns?
DESeq2
tximportData
tximpor
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
Alexander
• 0
0
votes
1
reply
1.1k
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
pthom010
• 0
0
votes
7
replies
2.2k
views
Problem with Tximport
tximportData
tximport
4.3 years ago
agoesmartini
• 0
0
votes
1
reply
1.2k
views
How to use tx import on output of abundance file
tximportData
tximport
updated 4.5 years ago by
Kevin Blighe
★ 4.0k • written 4.5 years ago by
Julie
• 0
0
votes
4
replies
1.6k
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 5.1 years ago by
Michael Love
43k • written 5.1 years ago by
slouis
• 0
1
vote
2
replies
1.3k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
6.6 years ago
fcuy047
• 0
1
vote
2
replies
1.4k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
Stanley Yang
• 0
1
vote
8
replies
37k
views
How to create tx2gene.gencode.v27.csv
tximportdata
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
mmokrejs
• 0
2
votes
6
replies
2.0k
views
[DESeq2] Different results from tutorial
deseq2
tximportdata
tximport
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
changhan1110
• 0
0
votes
1
reply
2.9k
views
could not find function "tximport"
tximportdata
updated 7.2 years ago by
Gordon Smyth
52k • written 7.2 years ago by
s.corley
▴ 30
0
votes
9
replies
4.0k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 7.3 years ago by
hauken_heyken
▴ 80 • written 8.9 years ago by
jarod_v6@libero.it
▴ 40
0
votes
3
replies
16k
views
Problem installing tximportData
tximportdata
8.2 years ago
elg
• 0
3
votes
5
replies
3.1k
views
txImport: a gene seems missing from the sample data
txImportData
txImport
updated 4.3 years ago by
James W. MacDonald
68k • written 8.2 years ago by
alexlok
• 0
1
vote
1
reply
2.0k
views
How to remove genes with 0 counts in tximport?
tximport
deseq
tximportdata
deseq2
updated 8.3 years ago by
Michael Love
43k • written 8.3 years ago by
Peter Alto
▴ 20
0
votes
7
replies
2.1k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 8.9 years ago by
Michael Love
43k • written 8.9 years ago by
jarod_v6@libero.it
▴ 40
25 results • Page
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Comment: Heatmap of rnaseq data with z-score scale
by
Paul Harrison
▴ 110
There can be considerable differences between datasets just due to different handling, sequencing method, batch effects, etc etc, and this …
Comment: Memory issue while using "quickcluster" and "computeSumFactors" functions on sin
by
ATpoint
★ 4.8k
What is lac cells? You mean 7000-9000 cells? Please check first that the function runs OOM even without any of these multicore options set.…
Comment: parameters of filterByExpr
by
caroline.zanchi
▴ 10
It worked, I think I finally understand and accept that fact. Sorry and thank you again !
Comment: parameters of filterByExpr
by
Gordon Smyth
52k
You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…
Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi
by
Gordon Smyth
52k
modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…
Votes
Comment: Heatmap of rnaseq data with z-score scale
Answer: parameters of filterByExpr
Comment: Heatmap of rnaseq data with z-score scale
Answer: LogFC values in edgeR - w/wo intercept
How to formulate 2 factor nested design in DESeq2
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