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tximportData
•
reset
0
votes
4
replies
315
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
12 days ago • updated 11 days ago
JG13
• 0
2
votes
9
replies
1.3k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
11 months ago
Ndimensional
▴ 20
0
votes
2
replies
716
views
tximport error in reading salmon output files?
tximport
tximportData
updated 4 months ago by
Matteo
• 0 • written 12 months ago by
barrypraveen
• 0
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
18 months ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
1.0k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
20 months ago • updated 19 months ago
duhwa.lee
• 0
0
votes
4
replies
1.2k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
23 months ago
uhlkatie
• 0
2
votes
3
replies
991
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
Luisa
• 0
0
votes
3
replies
953
views
tximport fails when RSEM output options produce files with additional columns?
DESeq2
tximportData
tximpor
updated 2.9 years ago by
Michael Love
42k • written 2.9 years ago by
Alexander
• 0
0
votes
1
reply
881
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 3.1 years ago by
Michael Love
42k • written 3.1 years ago by
pthom010
• 0
0
votes
7
replies
1.8k
views
Problem with Tximport
tximportData
tximport
3.4 years ago
agoesmartini
• 0
0
votes
1
reply
944
views
How to use tx import on output of abundance file
tximportData
tximport
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
Julie
• 0
0
votes
4
replies
1.2k
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 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
slouis
• 0
1
vote
2
replies
1.1k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
5.7 years ago • updated 5.6 years ago
fcuy047
• 0
1
vote
2
replies
1.2k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 5.7 years ago by
Michael Love
42k • written 5.7 years ago by
Stanley Yang
• 0
1
vote
8
replies
33k
views
How to create tx2gene.gencode.v27.csv
tximportdata
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
mmokrejs
• 0
2
votes
6
replies
1.7k
views
[DESeq2] Different results from tutorial
deseq2
tximportdata
tximport
updated 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
changhan1110
• 0
0
votes
1
reply
2.4k
views
could not find function "tximport"
tximportdata
updated 6.3 years ago by
Gordon Smyth
51k • written 6.3 years ago by
s.corley
▴ 30
0
votes
9
replies
3.5k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 6.4 years ago by
hauken_heyken
▴ 80 • written 8.0 years ago by
jarod_v6@libero.it
▴ 40
0
votes
3
replies
14k
views
Problem installing tximportData
tximportdata
7.3 years ago
elg
• 0
3
votes
5
replies
2.7k
views
txImport: a gene seems missing from the sample data
txImportData
txImport
updated 3.4 years ago by
James W. MacDonald
66k • written 7.3 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 7.4 years ago by
Michael Love
42k • written 7.4 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 7.9 years ago by
Michael Love
42k • written 7.9 years ago by
jarod_v6@libero.it
▴ 40
22 results • Page
1 of 1
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Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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