Showing : txImportData • reset
2
votes
9
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785
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
5 months ago • updated 4 months ago Ndimensional ▴ 20
0
votes
2
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408
views
tximport error in reading salmon output files?
tximport tximportData
5 months ago barrypraveen • 0
2
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3
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901
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
12 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
669
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
13 months ago duhwa.lee • 0
0
votes
4
replies
860
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
17 months ago uhlkatie • 0
2
votes
3
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800
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 21 months ago by 41k • written 21 months ago by • 0
0
votes
3
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762
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tximport fails when RSEM output options produce files with additional columns?
DESeq2 tximportData tximpor
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
0
votes
1
reply
743
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Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
0
votes
7
replies
1.5k
views
Problem with Tximport
tximportData tximport
2.8 years ago agoesmartini • 0
0
votes
1
reply
806
views
How to use tx import on output of abundance file
tximportData tximport
updated 3.0 years ago by 3.9k • written 3.0 years ago by • 0
0
votes
4
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917
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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 3.6 years ago by 41k • written 3.6 years ago by • 0
1
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2
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935
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
5.1 years ago fcuy047 • 0
1
vote
2
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1.0k
views
trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
1
vote
8
replies
31k
views
How to create tx2gene.gencode.v27.csv
tximportdata
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
2
votes
6
replies
1.4k
views
[DESeq2] Different results from tutorial
deseq2 tximportdata tximport
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
0
votes
1
reply
2.2k
views
could not find function "tximport"
tximportdata
updated 5.8 years ago by 48k • written 5.8 years ago by ▴ 30
0
votes
9
replies
3.3k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte tximportData
updated 5.8 years ago by ▴ 80 • written 7.4 years ago by ▴ 40
0
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3
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12k
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Problem installing tximportData
tximportdata
6.7 years ago elg • 0
3
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5
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2.5k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 2.9 years ago by 64k • written 6.7 years ago by • 0
0
votes
1
reply
1.6k
views
How to remove genes with 0 counts in tximport?
tximport deseq tximportdata deseq2
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 10
0
votes
7
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1.5k
views
PCA results different from th same sample but different counting method
deseq2 pca tximportdata htseqcounts
updated 7.4 years ago by 41k • written 7.4 years ago by ▴ 40
21 results • Page 1 of 1
Recent ...
Replies
Comment: Unlog transformed data in DESeq2 by Gordon Smyth 48k
The RUVIII people themselves use limma ( https://doi.org/10.1093/nar/gkz433 ). But please, post your question as a question. That would be …
Comment: DESeq2 - groups with biological replicates from the same patient by Oscar • 0
Yes I see that. So, to expand, if strong grouping IS seen, then the ```~condition``` approach is not appropriate, as will likely lead to po…
Comment: DESeq2 - groups with biological replicates from the same patient by Oscar • 0
This seems a very odd response to what seemed to be a very reasonable question
Comment: DESeq2 - groups with biological replicates from the same patient by Oscar • 0
I'm not using Chat GPT. I've been discussing at length this issue of having multiple samples derived from the same patients with many colle…
Comment: DESeq2 - groups with biological replicates from the same patient by Kevin Blighe 3.9k
No, it's more important to solve broader issues. >10 million children go hungry every day in the USA. Controlling for Type 1 error will not…
Votes
Answer: trying to add SingleR label to Seurat Object fails
Comment: DESeq2 - groups with biological replicates from the same patient
Answer: EdgeR: Exact test and glmQLFTest produce very different results
Answer: limma::voom vs edgeR::voomLmFit - when to use?
A: DSS understanding delta option and posterior probability
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