Showing : tximport • reset
0
votes
4
replies
1.1k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
26 days ago • updated 21 days ago Sofia • 0
0
votes
4
replies
550
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
6 weeks ago • updated 5 weeks ago Nicholas • 0
0
votes
11
replies
912
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 3 months ago by • 0 • written 3 months ago by • 0
1
vote
2
replies
759
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
4 months ago georgii.vdovin • 0
4
votes
5
replies
967
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
5 months ago LuciaNhu • 0
0
votes
2
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526
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
2
replies
523
views
tximport data import
tximport
updated 7 months ago by 43k • written 7 months ago by • 0
1
vote
2
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1.0k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
8 months ago grothmn • 0
1
vote
2
replies
2.5k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 10 months ago by ▴ 40 • written 5.5 years ago by • 0
0
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4
replies
739
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Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
10 months ago JG13 • 0
2
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3
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2.0k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.5 years ago by ▴ 50
6
votes
7
replies
3.5k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 3 months ago by 52k • written 4.9 years ago by ▴ 20
12 results • Page 1 of 1
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Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - I appreciate the mathematical explanation and link to Dr. Phipson's thesis!
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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