machine-learning
machine-learning copied to clipboard
cognoma
Machine learning for Project Cognoma
http://oncokb.org contains [418 genes](http://oncokb.org/#/genes) with varying levels of evidence for their role as cancer targets. This is a great list of genes to fit classifiers for.
[BRAF V600E](http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=476) mutations are common in several cancer types, including [melanoma](https://www.mycancergenome.org/content/disease/melanoma/braf/54/). This mutation is also present in about 8% of [colorectal cancer patients](https://doi.org/10.4137/BIC.S25248) (COAD and READ). However, there is emerging...
It might be useful to store the files currently being downloaded by `1.download.ipynb` on git's large file storage. That way we can eliminate `1.download.ipynb` and have the data files under...
I'm still working my way through the paper published by @gwaygenomics, @allaway and @cgreene, but it made me think of an issue that I believe we should try to deal...
Since there often are new members who join us, it seems a good idea to provide a quick guide for the machine learning work for Cognoma. The `README.md` file has...
I think it's likely that there is a general expression pattern for how mutated a tumor is. For example, super mutated tumors may have wacky gene expression, solely because they're...
It seems that some of the most interesting genes to predict using expression will be genes that have targeted therapies. These genes are ideal, because we may be able identify...
In the August 26 meetup, we discussed having each team member in the machine learning group claim an algorithm. We've made lot's of progress on the example notebook (`1.TCGA-MLexample.ipynb`) since...
There are several research papers and webpages that can be helpful to the cognoma task. Maybe I missed it, but I am not aware of any other issue that addresses...
This issue is a follow-up of the results obtained for different genes #52 . It is still not clear why few oncogenes produced such bad results. Before analyzing genes themselves,...