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tximportdata
•
reset
1
vote
2
replies
267
views
The default value of 'abundanceCol'
tximportData
4 months ago • updated 3 months ago
Jinghua
• 0
0
votes
1
reply
427
views
Error: lexical error: invalid char in json text (alevin-seurat)
tximpo
tximportData
alevinQC
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
ptlsugam
• 0
0
votes
2
replies
831
views
Need new version : tx2gene.gencode.v47.csv
tximportData
12 months ago • updated 6 months ago
Gaurav
• 0
4
votes
5
replies
1.4k
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
13 months ago
LuciaNhu
• 0
0
votes
4
replies
999
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
18 months ago
JG13
• 0
2
votes
9
replies
2.4k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
2.4 years ago
Ndimensional
▴ 20
0
votes
2
replies
1.2k
views
tximport error in reading salmon output files?
tximport
tximportData
updated 22 months ago by
Matteo
• 0 • written 2.5 years ago by
barrypraveen
• 0
2
votes
3
replies
2.2k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
3.0 years ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
1.8k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
3.1 years ago
duhwa.lee
• 0
0
votes
4
replies
1.9k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
3.4 years ago
uhlkatie
• 0
2
votes
3
replies
1.5k
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 3.8 years ago by
Michael Love
43k • written 3.8 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 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
Alexander
• 0
0
votes
1
reply
1.2k
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
pthom010
• 0
0
votes
7
replies
2.4k
views
Problem with Tximport
tximportData
tximport
4.9 years ago
agoesmartini
• 0
0
votes
1
reply
1.3k
views
How to use tx import on output of abundance file
tximportData
tximport
updated 5.1 years ago by
Kevin Blighe
★ 4.0k • written 5.1 years ago by
Julie
• 0
0
votes
4
replies
1.9k
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 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
slouis
• 0
1
vote
2
replies
1.5k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
7.1 years ago
fcuy047
• 0
1
vote
2
replies
1.6k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
Stanley Yang
• 0
1
vote
8
replies
38k
views
How to create tx2gene.gencode.v27.csv
tximportdata
updated 7.5 years ago by
Michael Love
43k • written 7.5 years ago by
mmokrejs
• 0
2
votes
6
replies
2.2k
views
[DESeq2] Different results from tutorial
deseq2
tximportdata
tximport
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
changhan1110
• 0
0
votes
1
reply
3.0k
views
could not find function "tximport"
tximportdata
updated 7.8 years ago by
Gordon Smyth
53k • written 7.8 years ago by
s.corley
▴ 30
0
votes
9
replies
4.3k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 7.9 years ago by
hauken_heyken
▴ 80 • written 9.5 years ago by
jarod_v6@libero.it
▴ 40
0
votes
3
replies
16k
views
Problem installing tximportData
tximportdata
8.7 years ago
elg
• 0
3
votes
5
replies
3.2k
views
txImport: a gene seems missing from the sample data
txImportData
txImport
updated 4.9 years ago by
James W. MacDonald
68k • written 8.8 years ago by
alexlok
• 0
1
vote
1
reply
2.2k
views
How to remove genes with 0 counts in tximport?
tximport
deseq
tximportdata
deseq2
updated 8.8 years ago by
Michael Love
43k • written 8.8 years ago by
Peter Alto
▴ 20
0
votes
7
replies
2.3k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 9.4 years ago by
Michael Love
43k • written 9.4 years ago by
jarod_v6@libero.it
▴ 40
26 results • Page
1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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