User: assaron

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assaron60
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assaron
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Posts by assaron

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Comment: C: Statistic for GSA
... fgsea works downstream of gene ranking, so it's impossible to do sample permutations and only gene permutations are used for the test. ...
written 7 weeks ago by assaron60
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Answer: A: Direction aware fgsea test
... Hi,  The GSEA test is itself directional, so you don't need to invert sign yourself. There are pathways with positive and negative enrichment scores (ES or NES). May be the example that goes with fgsea is not the best one, as the top-regulated pathways go in the same direction, but still there are ...
written 9 weeks ago by assaron60
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Comment: C: Chipseeker is unavabile on Linux CentOS7 ?
... Have you resolved the issue? I got similar problem recently and setting CXX1X environment variable for C++ compiler did help me. ...
written 4 months ago by assaron60
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Comment: C: Chipseeker is unavabile on Linux CentOS7 ?
... It seem like something eats up compiler command line: the line "I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG  -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c RcppExports.cpp -o RcppExports.o` should start with "g++ -I/usr/lib/..." or something li ...
written 4 months ago by assaron60
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Comment: C: pre-ranked GSEA within R?
... Please, check out the package fgsea (http://bioconductor.org/packages/devel/bioc/html/fgsea.html) it now has a very fast algorithm for pre-ranked GSEA. If you are not using devel version of Bioconductor you can install it from github using devtools::install_github("ctlab/fgsea") ...
written 7 months ago by assaron60
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Answer: A: pre-ranked GSEA within R?
... I think it might be of interest, that I implemented a fast algorithm for pre-ranked GSEA as an R-package "fgsea" which is available at Bioconductor (http://bioconductor.org/packages/fgsea) in devel-version and on GitHub (https://github.com/ctlab/fgsea). When I say "fast", I mean a ten thousand perm ...
written 7 months ago by assaron60
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Comment: C: pre-ranked GSEA within R?
... Yes, I mainly worked on improving gsea statistic performance. There is also a branch fastGSEA in the github repo that has even faster version, however it's slightly different from the original formulation. ...
written 11 months ago by assaron60
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Comment: C: pre-ranked GSEA within R?
... Hello Pekka and Daniel,  Sorry for picking up the old thread, I just wanted to let you know that if you are still interested in this, I did some rewrite of piano sampling function, now it can do 10000 permutations for ~900 reactome pathways in about 10 min in a single thread. It did not went into t ...
written 12 months ago by assaron60

Latest awards to assaron

Scholar 12 months ago, created an answer that has been accepted. For A: Direction aware fgsea test
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: pre-ranked GSEA within R?

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