Releases · Sage-Bionetworks/GENIE-Sponsored-Projects

What's Changed

Add monitor cron by @thomasyu888 in #2
Add new users to be notified by @xindiguo in #3
Add stats team to the list by @xindiguo in #4
Add code to create BPC mappings by @thomasyu888 in #5
Update clinical supp survival file by @thomasyu888 in #6
Create separate survival treatment file by @thomasyu888 in #8
Add other SP code by @thomasyu888 in #7
Use unified mapping by @thomasyu888 in #10
Make sure to exclude regimen drugs that contain the str investigational drug by @thomasyu888 in #11
Add support for priority column for clinical files by @thomasyu888 in #12
Add in retraction policy by @thomasyu888 in #13
Update version of table to use by @thomasyu888 in #15
Allow for this respository to be installed by @thomasyu888 in #17
Update mapping version by @thomasyu888 in #16
hardcode mapping for laterality by @thomasyu888 in #19
regimen abbreviation formed from all words of a drug by @hhunterzinck in #22
drug regimen abbreviations with ncit codes by @hhunterzinck in #24
Support PANC cohort by @thomasyu888 in #21
dockerize geniesp by @hhunterzinck in #25
Back compatibility by @hhunterzinck in #26
Run black ./geniesp to lint code by @thomasyu888 in #36
Add in new package setup by @thomasyu888 in #35
Add contribution guide by @thomasyu888 in #34
Edit setup by @thomasyu888 in #39
add bladder class by @hhunterzinck in #40
validation script for bpc to cbio mapping file by @hhunterzinck in #33
adapt new variable names and cohorts by @hhunterzinck in #43
add functionality and checks to mapping file validation by @hhunterzinck in #46
Remove null start dates by @thomasyu888 in #47
fix panc files by @hhunterzinck in #50
Add code of conduct by @thomasyu888 in #57
Remove low-memory pandas warning by @thomasyu888 in #54
Use pd.concat instead of dataframe.append by @thomasyu888 in #55
update genomic data release file by @hhunterzinck in #58
account for missing AGENT by @hhunterzinck in #60
fix hack by @hhunterzinck in #62
update mapping table by @hhunterzinck in #64
Create metadata files by @thomasyu888 in #38
Don't create folder if staging by @thomasyu888 in #56
additional validation checks for bpc to cbio portal mapping file by @hhunterzinck in #66
add troubleshooting guide first draft by @hhunterzinck in #68
update derived variable name and other misc fixes by @hhunterzinck in #69
update nsclc 2.0-public column header by @hhunterzinck in #71
cohort generic doc links for meta study file and minor fixes by @hhunterzinck in #74
fix inconsistencies between cBioPortal and clinical files by @hhunterzinck in #76
update meta study desc by @hhunterzinck in #81
remove data catalog dependency by @hhunterzinck in #82
update cbio panc column name by @hhunterzinck in #91
modify timeline dx generation by @hhunterzinck in #93
sor col name reference by @hhunterzinck in #97
rad therapy dataset name and mapping table updates by @hhunterzinck in #99
remove gh-action by @thomasyu888 in #100
[IBCDPE-261] Make sure blank values are filled with NA by @thomasyu888 in #102
Update main genie release used to 12.0-public by @thomasyu888 in #103
Change AGE_AT_SEQUENCING to integer by @thomasyu888 in #104
[GEN-90] Add nextflow wf by @thomasyu888 in #105
[GEN-261] retract samples from clinical survival treatment file by @thomasyu888 in #106
[GEN-264] Rename the seg file to be more in line with other cbioportal files by @thomasyu888 in #107
[GEN-286] Make sure meta seg file is named correctly by @thomasyu888 in #108
[GEN-94] Add initial commit to get start date by @thomasyu888 in #109
[GEN-335] sequence file drop duplicates by @thomasyu888 in #110
[GEN-384] Include data sv in bpc releases by @thomasyu888 in #111
function per file by @hhunterzinck in #95
[GEN-507] Add in performance status variable by @thomasyu888 in #112
[GEN-460] Staging runs should upload to a different Synapse folder by @thomasyu888 in #113
[GEN-628] Update PFS status variables by @thomasyu888 in #114
[GEN-746] timeline performance status RESULT column must be integers by @thomasyu888 in #115
[GEN-778] Add timeline treatment to NSCLC by @thomasyu888 in #117
[GEN-766, GEN-870] Retract using release files and use consortium release by @thomasyu888 in #116
Update README.md by @Chelsea-Na in #120
[GEN-889] Updating validate_map.py by @Chelsea-Na in #122
[GEN-848, GEN-860] Add in ECOG values by @thomasyu888 in #119
[GEN-950] Support NA values in AGE_AT_SEQUENCING by @thomasyu888 in #123
[GEN-949] Add in retraction table synids by @thomasyu888 in #124
[GEN-954] Remove GRS by @thomasyu888 in #125
[GEN-1004] Update bpc_redcap_export_mapping.py by @Chelsea-Na in #127
[GEN-1083] use 15.4-release by @thomasyu888 in #129
[GEN-1062] Use GRS instead of data dictionary for drug mapping by @thomasyu888 in https://github.com/Sage-Bionetworks/GENIE...