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2022-12-04create_edges_mixtool.R: enable command line argumentHui Lan
2022-11-20Fix the following errors while running create_edges0B.pyHui Lan
~/brain/Code$ python3 update_rnaseq_info_json.py Error in library(Rtsne) : there is no package called ‘Rtsne’ ~/brain/Code$ Rscript correlation_per_tissue.R Error in quantile.default(sd.1) : missing values and NaN's not allowed if 'na.rm' is FALSE
2022-11-20update_network.py: no longer need to redirect to fileHui Lan
2022-11-11correlation_per_group_fixed_number.R: fix 'argument is of length zero' error.Hui Lan
2022-11-09correlation_per_group_fixed_number.R: simplifyHui Lan
2022-11-07update_network_by_force.py: back up the edge file once a month.Hui Lan
2022-11-05Make correlation_per_group_fixed_number.R work, and update its upstream ↵Hui Lan
scripts (i.e., assign_tissue.py and refine_tissue.py).
2022-10-13configure.py: update TPM renewal intervalHui Lan
2022-10-10configure.py: update the value of BUILDRMATRIX_RENEW_INTERVALHui Lan
2022-10-09Shorten config variable name, remove 'PARAMETER_FOR_'Hui Lan
2022-10-09merge_edges.py: do not use HTML tags if the info is written to databaseHui Lan
2022-10-09merge_edges.py: removed a commented-out line.Hui Lan
2022-10-07Change the place used to store downloaded raw RNASeq data.Hui Lan
2022-10-05configure.py: be more specific about 'memory' - not computer memory, but ↵Hui Lan
brain memory.
2021-07-27configure.py: double daily downloads.Hui Lan
2021-07-25utils.py: the statistics line must be inside the with context manager in ↵Hui Lan
order to be written to the file edges-diff.txt.
2021-07-24utils.py: add info such as number of new edges and modification time.Hui Lan
2021-07-23utils.py: header for edges-diff.txt.Hui Lan
2021-07-23merge_edges.py: include fewer edges to prevent running out of memory.Hui Lan
2021-07-20update_network_by_force.py: get the difference in edges (yesterday vs. today).Hui Lan
2021-07-18configure.py: always build new TPM.txt.Hui Lan
2021-07-18configure.py: change the update interval.Hui Lan
2021-04-24merge_edges.py: use the most recent 365 edge files (to handle out-of-memory ↵Hui Lan
problem).
2021-02-18make_target_tf.py and param4net.py: add an option EXISTING_TARGET_TF_PAIRS ↵Hui Lan
in parameter_for_net.txt to specify locations of existing Target-TF pairs.
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 ↵Hui Lan
has been checked using isvalid.
2021-02-16make_target_tf_agris.py: refactor code, and include tf-target pairs from the ↵Hui Lan
latest osu AtRegNet data.
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
used.
2021-02-10download_and_map.py: simplify function read_ena_data_info_json such that it ↵Hui Lan
includes all info.
2021-02-10download_and_map.py: adpat this script to use the latest ↵Hui Lan
rnaseq_info_database.json file.
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
2021-02-06Move 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
quant.sf.
2020-10-27buildRmatrix.py: use a string to store the max expression level from ↵Hui Lan
isoforms (revision).
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 ↵Hui Lan
script could run out of memory space (7GB) when there are more than 1000 RNA-seq samples.
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 ↵Hui Lan
AT3G09600_AT1G49720_0.html correct (revision 2).
2020-08-15html_network.py: make URL for edge information such as ↵Hui Lan
AT3G09600_AT1G49720_0.html correct (revision).
2020-08-14start_webapp.py and util_networkx.py: remove them (they are in ↵Hui Lan
/var/www/brain/brain).
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