PNNL-CompBio coderdata issues

PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.

BSD 3-Clause "New" or "Revised" License

9 stars 3 forks source link

issues

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added instructions for synapse download

#179 sgosline opened 2 days ago
6
Column labels as multiple rows in experiments dataframe

#178 nkoussa opened 2 days ago
1
BeatAML Drugs not generating correctly.

#177 jjacobson95 opened 2 days ago
1
added fix for copy number

#176 sgosline closed 3 days ago
0
Parallelization of build_all.py

#175 jjacobson95 opened 6 days ago
0
Inconsistency in copy_call values

#174 nkoussa closed 3 days ago
2
Nci60 and other fixes

#173 sgosline closed 1 week ago
1
cptac samples failing when running from build_all.py

#172 jjacobson95 closed 1 week ago
1
broad_sanger_omics samples generation error

#171 jjacobson95 closed 1 week ago
2
not enough free space error when running python build/build_all.py --docker

#170 coleslaw481 closed 1 week ago
1
Local build doesn't work without synapse login permissions

#169 sgosline closed 1 week ago
0
HTTPS_PROXY key error when trying to run python build/build_all.py --docker

#168 coleslaw481 closed 1 week ago
2
No 00-buildGeneFile.R file in broad_sanger

#167 coleslaw481 closed 1 week ago
1
unable to build docker described in broad_sanger/README.md

#166 coleslaw481 closed 1 week ago
3
HCMI Samples file is skipping some improve_sample_id values.

#165 jjacobson95 opened 2 weeks ago
0
Broad_Sanger Samples File has duplicate improve_sample_ids and maybe more issues

#164 jjacobson95 opened 2 weeks ago
1
MPNST datasets' "improve_sample_id" not aligning with the coderdata version 0.1.26

#163 moonchangin opened 2 weeks ago
2
tutorial missing download step

#162 sgosline opened 2 weeks ago
0
broad_sanger experiments file not concatenatated correctly upon creation

#161 jjacobson95 closed 1 week ago
5
broad_sanger samples file has quotes around all values - (breaking Polars during testing)

#160 jjacobson95 opened 2 weeks ago
5
Convert Python Package from Pandas to Polars

#159 jjacobson95 opened 2 weeks ago
8
Add multi-processing to drug curve fitting

#158 jjacobson95 closed 1 week ago
1
Docker cleanup

#157 sgosline closed 2 weeks ago
0
Update README to have contributing guide

#156 sgosline opened 3 weeks ago
0
Update local build script for efficiency and upload

#155 sgosline opened 3 weeks ago
0
Ensure all datasets have the same transcriptomics normalization metric

#154 jjacobson95 opened 3 weeks ago
3
MPNST sample data does not match model types.

#153 jjacobson95 closed 3 weeks ago
0
Docker cleanup to reduce image size and standardize builds

#152 sgosline closed 3 weeks ago
0
New pyyaml fix

#151 jjacobson95 closed 3 weeks ago
0
Fixed pyyaml requirement

#150 jjacobson95 closed 3 weeks ago
3
Docs, visualization, stats generation, and tutorials updated.

#149 jjacobson95 closed 3 weeks ago
1
Update doc page with current datasets

#148 sgosline closed 3 weeks ago
4
Typos on Drug Response Tutorial page

#147 briankarlberg closed 3 weeks ago
0
consider adding PDX data

#146 sgosline opened 1 month ago
3
pyaml not installed when running pip install coderdata

#145 coleslaw481 closed 3 weeks ago
0
add in kids first brain tumor cell line data

#144 sgosline opened 1 month ago
0
think about breaking up cell line data docker

#143 sgosline closed 3 weeks ago
0
populate drugs structure property table

#142 sgosline opened 1 month ago
3
Filter all omics data to only analyze 20k protein coding genes

#141 sgosline closed 3 weeks ago
0
Move drug curve calculation to multithreaded

#140 sgosline closed 1 week ago
0
add in new NCI60 and alter time treatment

#139 sgosline closed 1 week ago
2
mpnst Drugs file does not include drug synonyms

#138 jjacobson95 closed 3 weeks ago
0
Drop NA values in Broad_Sanger Mutation Data

#137 jjacobson95 closed 2 weeks ago
0
Drop NA values in Broad_Sanger Copy Number Data

#136 jjacobson95 closed 2 weeks ago
0
Drop NA values in Broad_Sanger Transcriptomic Data

#135 jjacobson95 closed 2 weeks ago
0
BeatAML Drugs file does not include drug synonyms

#134 jjacobson95 closed 2 weeks ago
0
Drop NA values in CPTAC Transcriptomic Data

#133 jjacobson95 closed 2 weeks ago
0
Drop NA values in CPTAC Proteomics Data

#132 jjacobson95 closed 2 weeks ago
0
Drop NA values in CPTAC Copy Number Data

#131 jjacobson95 closed 2 weeks ago
0
Drop NA values in BeatAML Proteomics Data

#130 jjacobson95 closed 3 weeks ago
0