User: TriS
TriS • 3.5k
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Posts by TriS
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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 10 months ago by
TriS • 3.5k
0
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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 10 months ago by
TriS • 3.5k
1
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1
answer
648
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1
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... this might help:
https://www.hindawi.com/journals/abi/2017/1278932/
...
written 12 months ago by
TriS • 3.5k
0
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2
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817
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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 12 months ago by
TriS • 3.5k
0
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1
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2.5k
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... as comment to DAVID, it has been updated to the [6.8 version][1] on Oct 2016
[1]: https://david.ncifcrf.gov/ ...
written 12 months ago by
TriS • 3.5k
2
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0
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471
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0
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... 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 12 months ago by
TriS • 3.5k
1
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2
answers
817
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2
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... MeV is a good start
http://mev.tm4.org/#/welcome
...
written 12 months ago by
TriS • 3.5k
0
votes
1
answer
44k
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1
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... 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 13 months ago by
TriS • 3.5k
1
vote
1
answer
44k
views
1
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... check
class(clinical)
if it's a matrix, transform it into a data.frame ...
written 14 months ago by
TriS • 3.5k
1
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1
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535
views
1
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... 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 15 months ago by
TriS • 3.5k
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For artifact/false peaks visible in wiggle files
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For breakdancer - cfg creation and chi square problem
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For indel position in repetitive regions
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For breakdancer - cfg creation and chi square problem
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For filtering pileup file with samtools for SomaticSniper
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For A: How to split gene names in my list?
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For A: How to split gene names in my list?
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For C: limma results topTable vs toptable differ
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For C: limma results topTable vs toptable differ
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For A: How to check whether two genomic regions contact in 3D?
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