| #!/usr/bin/env python | |
| # fix t2t gff3 error | |
| # now the problem is ids for some start&stop condons/exons are not unique | |
| # 11/20/2022 | |
| import sys,gzip | |
| from collections import defaultdict | |
| def sep_info(info): |
| # ------ a python cell ------ | |
| %load_ext rpy2.ipython | |
| pd_df = pd_df.T | |
| # ------ an R cell ------ | |
| %%R -i pd_df | |
| # `-i pd_df` means access to the global variable pd_df | |
| r_df = do.something(pd_df) |
| # setup | |
| gcloud auth list | |
| gcloud config set compute/zone us-east1-b | |
| gcloud config set compute/region us-east1 | |
| # create an instance template | |
| cat << EOF > startup.sh | |
| #! /bin/bash | |
| apt-get update | |
| apt-get install -y nginx |
This Gist summarizes my work for the Reactome project "Query Reactome Data in R" during the Google Summer of Code 2020.
I would first like to begin by thanking my mentors Justin Cook, Joel Weiser, and Solomon Shorser for their guidance and support this summer. It was a privilege to learn from such a talented and experienced team.
The main objective was to create an interface in R to query data from the Reactome knowledgebase.
