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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
9 months ago
Ndimensional
▴ 20
0
votes
2
replies
639
views
tximport error in reading salmon output files?
tximport
tximportData
updated 11 weeks ago by
Matteo
• 0 • written 10 months ago by
barrypraveen
• 0
2
votes
3
replies
1.2k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
17 months ago • updated 16 months ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
908
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 • updated 17 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
947
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
910
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
838
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
pthom010
• 0
0
votes
7
replies
1.7k
views
Problem with Tximport
tximportData
tximport
3.2 years ago
agoesmartini
• 0
0
votes
1
reply
913
views
How to use tx import on output of abundance file
tximportData
tximport
updated 3.4 years ago by
Kevin Blighe
★ 3.9k • written 3.4 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 5.5 years ago by
Michael Love
41k • written 5.5 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
2.3k
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 6.2 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 7.1 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
1 of 1
Recent ...
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
marka
• 0
As a single dad in Australia, finding time to unwind is rare, but [Lincoln Casino][1] has become my go-to escape after putting the kids to …
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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