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tximportData
•
reset
1
vote
2
replies
223
views
The default value of 'abundanceCol'
tximportData
10 weeks ago
Jinghua
• 0
0
votes
1
reply
397
views
Error: lexical error: invalid char in json text (alevin-seurat)
tximpo
tximportData
alevinQC
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
ptlsugam
• 0
0
votes
2
replies
800
views
Need new version : tx2gene.gencode.v47.csv
tximportData
10 months ago • updated 4 months ago
Gaurav
• 0
4
votes
5
replies
1.3k
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
11 months ago
LuciaNhu
• 0
0
votes
4
replies
914
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
16 months ago
JG13
• 0
2
votes
9
replies
2.3k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
2.3 years ago
Ndimensional
▴ 20
0
votes
2
replies
1.2k
views
tximport error in reading salmon output files?
tximport
tximportData
updated 21 months ago by
Matteo
• 0 • written 2.3 years ago by
barrypraveen
• 0
2
votes
3
replies
2.1k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
2.9 years ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
1.7k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
3.0 years ago
duhwa.lee
• 0
0
votes
4
replies
1.8k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
3.3 years ago
uhlkatie
• 0
2
votes
3
replies
1.5k
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
Luisa
• 0
0
votes
3
replies
1.4k
views
tximport fails when RSEM output options produce files with additional columns?
DESeq2
tximportData
tximpor
updated 4.3 years ago by
Michael Love
43k • written 4.3 years ago by
Alexander
• 0
0
votes
1
reply
1.2k
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
pthom010
• 0
0
votes
7
replies
2.4k
views
Problem with Tximport
tximportData
tximport
4.7 years ago
agoesmartini
• 0
0
votes
1
reply
1.3k
views
How to use tx import on output of abundance file
tximportData
tximport
updated 4.9 years ago by
Kevin Blighe
★ 4.0k • written 4.9 years ago by
Julie
• 0
0
votes
4
replies
1.8k
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 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
slouis
• 0
1
vote
2
replies
1.4k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
7.0 years ago
fcuy047
• 0
1
vote
2
replies
1.5k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
Stanley Yang
• 0
1
vote
8
replies
38k
views
How to create tx2gene.gencode.v27.csv
tximportdata
updated 7.3 years ago by
Michael Love
43k • written 7.3 years ago by
mmokrejs
• 0
2
votes
6
replies
2.1k
views
[DESeq2] Different results from tutorial
deseq2
tximportdata
tximport
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
changhan1110
• 0
0
votes
1
reply
3.0k
views
could not find function "tximport"
tximportdata
updated 7.7 years ago by
Gordon Smyth
53k • written 7.7 years ago by
s.corley
▴ 30
0
votes
9
replies
4.2k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 7.7 years ago by
hauken_heyken
▴ 80 • written 9.3 years ago by
jarod_v6@libero.it
▴ 40
0
votes
3
replies
16k
views
Problem installing tximportData
tximportdata
8.6 years ago
elg
• 0
3
votes
5
replies
3.2k
views
txImport: a gene seems missing from the sample data
txImportData
txImport
updated 4.8 years ago by
James W. MacDonald
68k • written 8.6 years ago by
alexlok
• 0
1
vote
1
reply
2.1k
views
How to remove genes with 0 counts in tximport?
tximport
deseq
tximportdata
deseq2
updated 8.7 years ago by
Michael Love
43k • written 8.7 years ago by
Peter Alto
▴ 20
0
votes
7
replies
2.2k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 9.3 years ago by
Michael Love
43k • written 9.3 years ago by
jarod_v6@libero.it
▴ 40
26 results • Page
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Votes
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
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