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4 daysRetrieve more tissue information from read_experimentLan Hui
5 daysRetrieve more tissue informationLan Hui
6 daysFuther improve XML processing logicHui Lan
7 daysParse ENA records XML files. It seems that XML structure for experiment, ↵Hui Lan
study and sample has changed.
7 daysFix typo 'expriment' in 'read_expriment'Hui Lan
8 daysShow script name in the log line.Hui Lan
8 daysSave ENA records to XML files under Data/temp/Hui Lan
11 daysRun this file from time to time to get the most recent RNA-Seq records at ENAHui Lan
11 daysMaintenanceHui Lan
14 daysShow number of remaining RNA-Seq data to reflect remaining workHui Lan
14 daysRemove the line in configure.py that caused downloading not work for 4 daysHui Lan
2025-04-02Reverse download log lines and write them to a new file ↵Hui Lan
download_log_reversed.txt so that the most recent log line appears on the top. Purpose: easier to check log from the web browser.
2025-03-09Remove the experimental file killprocess.pyHui Lan
2025-03-09Kill wget if it takes too longHui Lan
2025-03-09Append DONE to the download log in case the downloading process cannot move ↵Hui Lan
on. Added two helper functions: age_of_file_in_hours() and append_done(). Ran dos2unix; that is why there are so many changes.
2025-03-09Sync changes made on my Ubuntu desktop machine i7-13700HHui Lan
2025-03-09configure.pyHui Lan
2024-08-28Pretty print JSONLan Hui
2024-08-26JSON file should look like '{key:value}' but not ['{key:value}']Lan Hui
2024-08-26Use R package jsonlite instead of rjson, to support the 'digits' option, ↵Lan Hui
which allows keeping fewer digits after decimal, thus saving disk storage space
2024-08-17[mergeTPM.py] correct grammar errorLan Hui
2024-08-17merge all TPM files and put the merged file in folder assembleLan Hui
2024-08-16Count all downloaded RUNsLan Hui
2024-08-11Required Python modulesLan Hui
2024-08-11Remove temporary fileLan Hui
2024-08-11dos2unixLan Hui
2024-08-10[create_edges0B.py] Correct Python script nameHui Lan
2024-08-10[create_edges0.py] Store edges in folder ../Data/history/edges/many_targetsHui Lan
2024-08-10[update_network.py] Do not generation json files for gene expression if not ↵Hui Lan
do webapp
2024-08-09[update_network.py] Simplify codeHui Lan
2024-08-08Improve memory efficency while building TPM.txtHui Lan
2024-08-07Use TPM_FILE instead of TPM_TABLEHui Lan
2024-08-07Fix error occurred while running update_network.pyHui Lan
2024-08-07[update_network.py] Rename FILE_TIMESTAMP to TIMESTAMP_FILEHui Lan
2024-08-07Review update_network.pyHui Lan
2024-08-07Put the definition of make_paths() in utils.py because multiple places use itHui Lan
2024-08-07Important files and directoriesHui Lan
2024-08-06update_network.py: delete the 'merge edge' stuff because this is the job of ↵Hui Lan
update_network_by_force.py
2024-08-06merge_edges.py: add some commentsHui Lan
2024-08-05update_network_by_force.py: improve code speedHui Lan
2024-08-05update_network_by_force.py: fix runtime errorHui Lan
2024-08-05update_network_by_force.py: review and make updatesHui Lan
2024-08-05Remove testlog.txt because it is no longer neededHui Lan
2024-08-05Update write_log_file() so that it put the most recent message on the top; ↵Hui Lan
remove duplicate write_log_file()
2024-08-04Do not record duplicate edges (to save space). May take longer to run.Hui Lan
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