User: TriS
TriS • 3.4k
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Posts by TriS
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37
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36k
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37
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... this code is a guideline, not a copy and paste document. I'd suggest you to read a bit more about basic R usage and survival analysis before digging into this. it'll be time well spent ...
written 4 months ago by
TriS • 3.4k
0
votes
37
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36k
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37
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... you have to group patients using the parameters you chose (i.e. groups) instead of gene expression altered/not altered.
I'd suggest you to read a bit more about basic survival analysis and how it works before digging into this one ...
written 4 months ago by
TriS • 3.4k
1
vote
1
answer
448
views
1
answers
... this might help:
https://www.hindawi.com/journals/abi/2017/1278932/
...
written 6 months ago by
TriS • 3.4k
0
votes
2
answers
566
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2
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Comment:
C: PCA Tools to analyse RNA-seq data
... the linked version is a web-based application. the desktop application is a standalone java-based version ...
written 6 months ago by
TriS • 3.4k
0
votes
1
answer
2.3k
views
1
answers
... as comment to DAVID, it has been updated to the [6.8 version][1] on Oct 2016
[1]: https://david.ncifcrf.gov/ ...
written 6 months ago by
TriS • 3.4k
2
votes
0
answers
347
views
0
answers
... affinity is a different thing that abundance.
if you look at the wiggle/bigbed files for your ChiSeq you can check "how much" binding you have. however, none of this will tell you the "strength" of binding. you need wet lab experiments mutating the binding site to determine that. ...
written 6 months ago by
TriS • 3.4k
1
vote
2
answers
566
views
2
answers
... MeV is a good start
http://mev.tm4.org/#/welcome
...
written 6 months ago by
TriS • 3.4k
0
votes
37
answers
36k
views
37
answers
... looks like you don't have a columns called
patient.bcr_patient_barcode
or it's empty, therefore you can't assign it to the variable you are creating.
...
written 7 months ago by
TriS • 3.4k
1
vote
37
answers
36k
views
37
answers
... check
class(clinical)
if it's a matrix, transform it into a data.frame ...
written 8 months ago by
TriS • 3.4k
1
vote
1
answer
404
views
1
answers
... for DE transcripts keep the biological replicates separated, align them separately and then calculate DETs/DEGs.
for SNPs I'd suggest to do a similar approach. call SNPs per each replicate and keep those common across biological replicates. ...
written 9 months ago by
TriS • 3.4k
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