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AgeCommit message (Expand)Author
2021-04-24merge_edges.py: use the most recent 365 edge files (to handle out-of-memory p...Hui Lan
2021-02-19QUICKSTART.rst: explain option EXISTING_TARGET_TF_PAIRS in parameter_for_net....Hui Lan
2021-02-18make_target_tf.py and param4net.py: add an option EXISTING_TARGET_TF_PAIRS in...Hui Lan
2021-02-18make_target_tf.py: format of target_tf.txt.Hui Lan
2021-02-16make_target_tf_agris.py: no longer need to check ID starts with AT, as it has...Hui Lan
2021-02-16make_target_tf_agris.py: refactor code, and include tf-target pairs from the ...Hui Lan
2021-02-10test.py: delete it as it is for temporary testing purpose only.Hui Lan
2021-02-10test.py: make it work.Hui Lan
2021-02-10download_and_map.py: fix name d not defined error.Hui Lan
2021-02-10download_and_map.py: remove function read_ena_data_info() as it is no longer ...Hui Lan
2021-02-10download_and_map.py: simplify function read_ena_data_info_json such that it i...Hui Lan
2021-02-10download_and_map.py: adpat this script to use the latest rnaseq_info_database...Hui Lan
2021-02-10parse_ena_xml.py: adapt the script to use the latest meta data.Hui Lan
2021-02-09update_network_by_force.py: move the position of the 'update done' log.Hui Lan
2021-02-09overlap.py: while.Hui Lan
2021-02-09update_network_by_force.py: compute overlap with AtRegNet.20210208.csv.Hui Lan
2021-02-09overlap.py: compare predicted edges with gold standard (osu AtRegNet.csv) edges.Hui Lan
2021-02-09update_network.py: code review.Hui Lan
2021-02-06brain.documentation/QUICKSTART.rst: update version info and change log.Hui Lan
2021-02-06brain.documentation/QUICKSTART.rst: a Ubuntu server.Hui Lan
2021-02-06brain.documentation/QUICKSTART.rst: specify the running environment.Hui Lan
2021-02-06update .gitignore such that it could track QUICKSTART.rst in brain.documentat...Hui Lan
2021-02-06update .gitignore such that it could track QUICKSTART.rst in brain.documentat...Hui Lan
2021-02-06Move edge files in edge_pool to /disk1/edge_pool to save space in the workspace.Hui Lan
2020-12-13make_parameter_rnaseq.py: if a line in quant.sf is not complete, ignore this ...Hui Lan
2020-10-27buildRmatrix.py: use a string to store the max expression level from isoforms...Hui Lan
2020-10-27buildRmatrix.py: use a string to store the max expression level from isoforms.Hui Lan
2020-10-21update_network.py: make TPM.txt.Hui Lan
2020-10-10buildRmatrix.py: use string instead of float to store TPM values. This scrip...Hui Lan
2020-08-27buildRmatrix.py: get max value eariler.Hui Lan
2020-08-27buildRmatrix.py: remove a redundant line.Hui Lan
2020-08-16html_network.py: make URL for edge information such as AT3G09600_AT1G49720_0....Hui Lan
2020-08-15html_network.py: make URL for edge information such as AT3G09600_AT1G49720_0....Hui Lan
2020-08-14start_webapp.py and util_networkx.py: remove them (they are in /var/www/brain...Hui Lan
2020-08-14html_network.py: make URL for edge information such as AT3G09600_AT1G49720_0....Hui Lan
2020-05-05update_netowrk_by_force.py: curl http://118.25.96.118/brain/before should be ...Hui Lan
2020-05-05update_netowrk_by_force.py: check why merge_edges.py does not fully work.Hui Lan
2020-05-04merge_edges.py: Remove 'May take a while.' Actually, after insertion speed i...Hui Lan
2020-05-04merge_edges.py: Remove colon after [merge_edges.py].Hui Lan
2020-05-04merge_edges.py: rename make_new_edge2. Remove 2.Hui Lan
2020-05-04merge_edges.py: make sqlite insert really fast. Commit in the end instead of...Hui Lan
2020-05-04merge_edges.py: string does not have isnumeric method.Hui Lan
2020-05-03download_and_map.py: when download_log.txt contains blank lines, this script ...Hui Lan
2020-05-03configure.py: fewer daily downloadsHui Lan
2020-05-02download_and_map.py: lower the requirement of available disk space to make do...Hui Lan
2020-04-04Modified .gitignoreHui Lan
2020-04-04Modified .gitignoreHui Lan
2020-03-27update_network_by_force.py: the number of %s should be the same as the number...Hui Lan
2020-03-27html_network.py: string like 'F3'H' will cause syntax error in JavaScript. js...Hui Lan
2020-03-27html_network.py: string like 'F3'H' will cause syntax error in JavaScript.Hui Lan
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