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[DNM] retrieve list of portal ids and filter input lists with it #68

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[DNM] retrieve list of portal ids and filter input lists with it #68

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Commits on Sep 2, 2022

  1. add steps to rm genes without portal pages

    @raynamharris
    raynamharris committed Sep 2, 2022
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  2. Merge branch 'main' into retrieve-pages

    @raynamharris
    raynamharris authored Sep 2, 2022
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  3. Update ci.yml

    @raynamharris
    raynamharris authored Sep 2, 2022
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Commits on Sep 8, 2022

  1. get ids from json moved to cfde_common

    @raynamharris
    raynamharris committed Sep 8, 2022
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  2. filter added to all gene scripts

    @raynamharris
    raynamharris committed Sep 8, 2022
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  3. update input to full list

    @raynamharris
    raynamharris committed Sep 8, 2022
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  4. filter anatomy compound disease protein

    @raynamharris
    raynamharris committed Sep 8, 2022
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  5. undo filter by genes in staging

    @raynamharris
    raynamharris committed Sep 8, 2022
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  6. all terms

    @raynamharris
    raynamharris committed Sep 8, 2022
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  7. combine and rename compound scripts

    @raynamharris
    raynamharris committed Sep 8, 2022
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  8. update gtex gene list

    @raynamharris
    raynamharris committed Sep 8, 2022
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Commits on Sep 9, 2022

  1. add rule to download id lists from portal

    @raynamharris
    raynamharris committed Sep 9, 2022
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  2. add id lists

    @raynamharris
    raynamharris committed Sep 9, 2022
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  3. add retrieve rule

    @raynamharris
    raynamharris committed Sep 9, 2022
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  4. add id lists

    @raynamharris
    raynamharris committed Sep 9, 2022
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  5. use id list for ref file

    @raynamharris
    raynamharris committed Sep 9, 2022
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  6. adds an if statement if file existst

    @raynamharris
    raynamharris committed Sep 9, 2022
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  7. Merge branch 'main' into retrieve-pages

    @raynamharris
    raynamharris authored Sep 9, 2022
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  8. Merge branch 'main' into retrieve-pages

    @raynamharris
    raynamharris authored Sep 9, 2022
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Commits on Sep 11, 2022

  1. [MRG] generate URLs for lists of valid IDs dynamically (#71) 

    * remove validate files that can be created automatically

* suggest changes to Snakefile

* remove retrieve-ids.sh

* add validation CSVs to all rules

* fix CURL
    @ctb
    ctb authored Sep 11, 2022
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  2. change error to wraning

    @raynamharris
    raynamharris committed Sep 11, 2022
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Commits on Sep 12, 2022

  1. export missing IDs to file not stderr

    @raynamharris
    raynamharris committed Sep 12, 2022
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  2. create file for logs

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    raynamharris committed Sep 12, 2022
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  3. a to w

    @raynamharris
    raynamharris committed Sep 12, 2022
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  4. add plot to make dir

    @raynamharris
    raynamharris committed Sep 12, 2022
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  5. now with csv file and plot with markdown totals for each widget

    @raynamharris
    raynamharris committed Sep 12, 2022
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  6. rm second filter step

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    raynamharris committed Sep 12, 2022
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  7. new rules

    @raynamharris
    raynamharris committed Sep 12, 2022
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  8. summary plots

    @raynamharris
    raynamharris committed Sep 12, 2022
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  9. now with thousands of ucds widgets, high res plots

    @raynamharris
    raynamharris committed Sep 12, 2022
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  10. now with thousands of ucds widgets, high res plots

    @raynamharris
    raynamharris committed Sep 12, 2022
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  11. testing new common functions, improved performance, better output

    @raynamharris
    raynamharris committed Sep 12, 2022
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  12. working for diseases

    @raynamharris
    raynamharris committed Sep 12, 2022
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  13. now working for disease

    @raynamharris
    raynamharris committed Sep 12, 2022
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  14. one more disease

    @raynamharris
    raynamharris committed Sep 12, 2022
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  15. matches disease

    @raynamharris
    raynamharris committed Sep 12, 2022
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  16. working for 1 anatomy script

    @raynamharris
    raynamharris committed Sep 12, 2022
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  17. rm duplicate id

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    raynamharris committed Sep 12, 2022
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  18. working for anatomy

    @raynamharris
    raynamharris committed Sep 12, 2022
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  19. some genes working

    @raynamharris
    raynamharris committed Sep 12, 2022
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  20. correct list

    @raynamharris
    raynamharris committed Sep 12, 2022
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  21. working for appyters

    @raynamharris
    raynamharris committed Sep 12, 2022
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  22. working for more genes

    @raynamharris
    raynamharris committed Sep 12, 2022
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  23. working for more genes

    @raynamharris
    raynamharris committed Sep 12, 2022
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  24. rm duplicate

    @raynamharris
    raynamharris committed Sep 12, 2022
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  25. add period

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    raynamharris committed Sep 12, 2022
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  26. rm duplicate for real

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    raynamharris committed Sep 12, 2022
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  27. back to shorter gene list for ucsd

    @raynamharris
    raynamharris committed Sep 12, 2022
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  28. use full not test file

    @raynamharris
    raynamharris committed Sep 12, 2022
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  29. formatting

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    raynamharris committed Sep 12, 2022
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  30. fix errors

    @raynamharris
    raynamharris committed Sep 12, 2022
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  31. fix error

    @raynamharris
    raynamharris committed Sep 12, 2022
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  32. updated output

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    raynamharris committed Sep 12, 2022
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Commits on Sep 13, 2022

  1. better plots

    @raynamharris
    raynamharris committed Sep 13, 2022
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  2. fixed error output

    @raynamharris
    raynamharris committed Sep 13, 2022
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Commits on Sep 16, 2022

  1. staging test

    @raynamharris
    raynamharris committed Sep 16, 2022
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