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txImportData
•
reset
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
10 months ago • updated 9 months ago
Ndimensional
▴ 20
0
votes
2
replies
659
views
tximport error in reading salmon output files?
tximport
tximportData
updated 3 months ago by
Matteo
• 0 • written 10 months ago by
barrypraveen
• 0
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
17 months ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
926
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
duhwa.lee
• 0
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
22 months ago
uhlkatie
• 0
2
votes
3
replies
958
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
919
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
846
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 2.9 years ago by
Michael Love
41k • written 3.0 years ago by
pthom010
• 0
0
votes
7
replies
1.7k
views
Problem with Tximport
tximportData
tximport
3.3 years ago
agoesmartini
• 0
0
votes
1
reply
922
views
How to use tx import on output of abundance file
tximportData
tximport
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 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 5.6 years ago by
Michael Love
41k • written 5.6 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
2.4k
views
could not find function "tximport"
tximportdata
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
s.corley
▴ 30
0
votes
9
replies
3.5k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 6.3 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 3.3 years ago by
James W. MacDonald
65k • written 7.2 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
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Votes
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
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