Admin: Marcel Ramos
Marcel Ramos ♦♦ 210
- Reputation:
- 210
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- United States
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- 2 days, 13 hours ago
- Joined:
- 3 years, 6 months ago
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- m***********@roswellpark.org
Posts by Marcel Ramos
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... Hey all, How does this commit look?
https://github.com/Bioconductor/RaggedExperiment/commit/9fdcfbf0779d3508af7ae0afc288f946758b60d6
Thanks, Marcel
...
written 5 weeks ago by
Marcel Ramos ♦♦ 210
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... Hi Mario,
I've checked this with the Bioconductor release version 3.7 and it works as well.
There may be something wrong with your installation.
Check that you're not mixing versions of packages.
Remove a couple of packages: remove.packages(c("BiocManager", "BiocVersion")).
Your biocLite("BiocUp ...
written 7 weeks ago by
Marcel Ramos ♦♦ 210
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... Hi Mario,
Can you please include your sessionInfo() ?
This works for me with Bioc-devel 3.8.
library(curatedTCGAData)
library(TCGAutils)
coad <- curatedTCGAData("COAD", "CN*", FALSE)
sampleTables(coad)
> sampleTables(coad)
$`COAD_CNASeq-20160128`
01 10 11
68 55 13
$`COAD_CNASNP-201601 ...
written 7 weeks ago by
Marcel Ramos ♦♦ 210
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94
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... 2) Yes, `curatedTCGAData` returns a `MultiAssayExperiment` data object.
...
written 7 weeks ago by
Marcel Ramos ♦♦ 210
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... Hi all,
I've looked into the issue and decided to contribute some code to add BiocCheck to
the Travis-CI builder.
I was finally able to get my code merged and to run a package check with BiocCheck.
Interestingly, my package is producing a false positive with BiocCheck but the build
is not erroring o ...
written 7 weeks ago by
Marcel Ramos ♦♦ 210
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... Hi Efstathios-Iason,
1)
As you may be aware, there are quite a number of resources for accessing TCGA data.
I would first point you to the curatedTCGAData Bioconductor package. This will give
you access to COAD data as MultiAssayExperiment objects.
You could also use curatedCRCData but you'd have ...
written 7 weeks ago by
Marcel Ramos ♦♦ 210
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121
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... Hi Benjamin,
It would be good to have Tiago Silva's input on this.
It seems like, at least for this case, the curation process considered the TNM stages
and coded for Stage IV
Here are a few other resources that you can use to check these variables
(many of which yield NA for pathologic_stage):
Geno ...
written 3 months ago by
Marcel Ramos ♦♦ 210
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123
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... Hi Ankita,
I was unable to reproduce the error. I suspect that it may have something to do with your internet connection.
Please check your connection settings and make sure that a firewall or VPN is not preventing you from
accessing the remote file.
There are other known issues for users of Wi ...
written 4 months ago by
Marcel Ramos ♦♦ 210
0
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... Hi Melissa,
Without a reproducible example, there is not much specific help that fellow Bioconductor users can provide.
If you have the ranges of those variants that have been merged, you can use findOverlaps to find the overlapping ranges in the original GRanges that correspond to those variant acc ...
written 4 months ago by
Marcel Ramos ♦♦ 210
0
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389
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... Hi Lloyd,
Thanks for posting a solution!
Best regards,
Marcel
...
written 4 months ago by
Marcel Ramos ♦♦ 210
Latest awards to Marcel Ramos
Supporter
12 weeks ago,
voted at least 25 times.
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: Querying specific TCGA datasets through the MultiAssayExperiment R package
Scholar
14 months ago,
created an answer that has been accepted.
For A: Classes and methods for working with segmented copy number data
Scholar
16 months ago,
created an answer that has been accepted.
For A: Classes and methods for working with segmented copy number data
Scholar
16 months ago,
created an answer that has been accepted.
For A: Classes and methods for working with segmented copy number data
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