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VAF Cutoff Filter Experiment for SNV callers #173

Merged
merged 176 commits into from
Oct 29, 2019
Merged

VAF Cutoff Filter Experiment for SNV callers #173

merged 176 commits into from
Oct 29, 2019

Commits on Sep 23, 2019

  1. Set up the set up

    Candace Savonen committed Sep 23, 2019
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  2. Add circle CI test and Docker config

    Candace Savonen committed Sep 23, 2019
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  3. Add some more comments

    Candace Savonen committed Sep 23, 2019
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  4. Merge remote-tracking branch 'upstream/master' into cansav09/snv-call… 

    …er_set_up
    Candace Savonen committed Sep 23, 2019
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  5. Set up Rprojroot for circle CI test to work better

    Candace Savonen committed Sep 23, 2019
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  6. Fixing Circle CI file.

    Candace Savonen committed Sep 23, 2019
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  7. Change read_tsv to data.table::fread for big file

    Candace Savonen committed Sep 23, 2019
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Commits on Sep 24, 2019

  1. read in the .gz file

    Candace Savonen committed Sep 24, 2019
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  2. push plot function changes

    Candace Savonen committed Sep 24, 2019
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Commits on Sep 25, 2019

  1. Fix an error

    Candace Savonen committed Sep 25, 2019
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Commits on Sep 26, 2019

  1. Merge branch 'master' into cansav09/snv-caller_set_up

    @cansavvy
    cansavvy authored Sep 26, 2019
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  2. Add missing package to Dockerfile

    Candace Savonen committed Sep 26, 2019
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  3. Reduce cosmic file to only the brain sample mutations

    Candace Savonen committed Sep 26, 2019
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  4. Update README with changes to cosmic file

    Candace Savonen committed Sep 26, 2019
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  5. re-updated Dockerfile

    Candace Savonen committed Sep 26, 2019
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  6. Ran a linter on set up script

    Candace Savonen committed Sep 26, 2019
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  7. Merge branch 'master' into cansav09/snv-caller_set_up

    @cansavvy
    cansavvy authored Sep 26, 2019
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  8. Comment out of date

    @cansavvy
    cansavvy authored Sep 26, 2019
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  9. Get rid of old WGX/WXS bed file set up

    Candace Savonen committed Sep 26, 2019
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Commits on Sep 27, 2019

  1. Merge branch 'master' into cansav09/snv-caller_set_up

    @cansavvy
    cansavvy authored Sep 27, 2019
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  2. Incorporate initial PR suggestions from @jashapiro and @cbethell

    Candace Savonen committed Sep 27, 2019
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  3. Push a working bash script

    Candace Savonen committed Sep 27, 2019
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  4. Add bash script to circle CI

    Candace Savonen committed Sep 27, 2019
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Commits on Sep 30, 2019

  1. Add usage section in README and change name of script

    Candace Savonen committed Sep 30, 2019
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  2. Merge branch 'master' into cansav09/snv_calculations

    @cansavvy
    cansavvy authored Sep 30, 2019
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  3. Add some more comments

    Candace Savonen committed Sep 30, 2019
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  4. Merge remote-tracking branch 'origin/cansav09/snv_calculations' into … 

    …cansav09/snv_calculations
    Candace Savonen committed Sep 30, 2019
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  5. Correct a couple things in the README

    Candace Savonen committed Sep 30, 2019
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  6. Get rid of remnant comment

    Candace Savonen committed Sep 30, 2019
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  7. Fix a typo!

    Candace Savonen committed Sep 30, 2019
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  8. Merge branch 'master' into cansav09/snv_calculations

    @cansavvy
    cansavvy authored Sep 30, 2019
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  9. Add Usage to the TOC

    Candace Savonen committed Sep 30, 2019
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  10. Merge branch 'master' into cansav09/snv_calculations

    @cansavvy
    cansavvy authored Sep 30, 2019
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Commits on Oct 1, 2019

  1. Add more documentation to the README

    Candace Savonen committed Oct 1, 2019
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  2. Update Circle CI

    Candace Savonen committed Oct 1, 2019
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  3. Push more exact bash script

    Candace Savonen committed Oct 1, 2019
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  4. Fix a couple issues with handling metadata file path

    Candace Savonen committed Oct 1, 2019
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  5. Get rid of dev remnants

    Candace Savonen committed Oct 1, 2019
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  6. Couple changes for readability

    Candace Savonen committed Oct 1, 2019
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  7. Merge branch 'master' into cansav09/snv_calculations

    @cansavvy
    cansavvy authored Oct 1, 2019
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  8. Add some things to README and get rid of part of bash that isn't there

    Candace Savonen committed Oct 1, 2019
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  9. Merge remote-tracking branch 'origin/cansav09/snv_calculations' into … 

    …cansav09/snv_calculations
    Candace Savonen committed Oct 1, 2019
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  10. Found dumb mistake

    Candace Savonen committed Oct 1, 2019
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  11. Changed [*] to [+]

    Candace Savonen committed Oct 1, 2019
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  12. I mean [*] to a [@] which makes more sense.

    Candace Savonen committed Oct 1, 2019
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Commits on Oct 2, 2019

  1. Merge branch 'master' into cansav09/snv_calculations

    @cansavvy
    cansavvy authored Oct 2, 2019
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Commits on Oct 3, 2019

  1. Fix some of the overwrite handling

    Candace Savonen committed Oct 3, 2019
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  2. Merge remote-tracking branch 'origin/cansav09/snv_calculations' into … 

    …cansav09/snv_calculations
    Candace Savonen committed Oct 3, 2019
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  3. Add template and report script

    Candace Savonen committed Oct 3, 2019
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  4. Add run_eval to bash script

    Candace Savonen committed Oct 3, 2019
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Commits on Oct 4, 2019

  1. Merge branch 'master' into cansav09/snv-add-eval

    @cansavvy
    cansavvy authored Oct 4, 2019
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  2. Get rid of dev remnants

    Candace Savonen committed Oct 4, 2019
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  3. Make better handling of strategy that is called but not there

    Candace Savonen committed Oct 4, 2019
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  4. Get rid of dev remnant again

    Candace Savonen committed Oct 4, 2019
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  5. Get rid of stray \

    Candace Savonen committed Oct 4, 2019
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  6. File got misplaced

    Candace Savonen committed Oct 4, 2019
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  7. Get rid of cosmic mutations without proper coordinates

    Candace Savonen committed Oct 4, 2019
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  8. Fixed a wrinkle with the COSMIC file

    Candace Savonen committed Oct 4, 2019
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  9. Merge branch 'master' into cansav09/snv-add-eval

    @cansavvy
    cansavvy authored Oct 4, 2019
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  10. re-run a linter on everything.

    Candace Savonen committed Oct 4, 2019
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  11. Merge remote-tracking branch 'origin/cansav09/snv-add-eval' into cans… 

    …av09/snv-add-eval
    Candace Savonen committed Oct 4, 2019
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  12. Couple more minor touches

    Candace Savonen committed Oct 4, 2019
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Commits on Oct 7, 2019

  1. Make set up files not run if they are already existing

    @cansavvy
    cansavvy authored Oct 7, 2019
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  2. Fix handling of COSMIC file creation

    @cansavvy
    cansavvy authored Oct 7, 2019
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Commits on Oct 8, 2019

  1. Incorporate @jashapiro 's suggestions

    Candace Savonen committed Oct 8, 2019
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  2. Add a few more @jashapiro suggestions

    Candace Savonen committed Oct 8, 2019
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  3. Merge branch 'master' into cansav09/snv-add-eval

    @cansavvy
    cansavvy authored Oct 8, 2019
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  4. Circle CI does not have a kitematic directory. Get rid

    Candace Savonen committed Oct 8, 2019
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  5. Merge remote-tracking branch 'origin/cansav09/snv-add-eval' into cans… 

    …av09/snv-add-eval
    Candace Savonen committed Oct 8, 2019
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  6. Make warning instead of stop

    Candace Savonen committed Oct 8, 2019
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  7. Missing ggplot2::

    Candace Savonen committed Oct 8, 2019
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  8. Remove reference files after use to try to reduce memory usage

    Candace Savonen committed Oct 8, 2019
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  9. Make one big mutate

    Candace Savonen committed Oct 8, 2019
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  10. Dumb extra comma

    Candace Savonen committed Oct 8, 2019
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Commits on Oct 9, 2019

  1. Add VAF_FILTER option and it's circle CI component

    Candace Savonen committed Oct 9, 2019
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  2. get rid of typo

    Candace Savonen committed Oct 9, 2019
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  3. Re-fix Circle CI file

    Candace Savonen committed Oct 9, 2019
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  4. Fix WXS if statement

    Candace Savonen committed Oct 9, 2019
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  5. Fix default Circle CI option

    Candace Savonen committed Oct 9, 2019
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  6. Make indels come last in the barplot

    Candace Savonen committed Oct 9, 2019
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  7. Fix order of barplot graph

    Candace Savonen committed Oct 9, 2019
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  8. Merge branch 'master' into cansav09/snv-add-eval

    @cansavvy
    cansavvy authored Oct 9, 2019
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  9. Add the comparison notebook

    Candace Savonen committed Oct 9, 2019
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  10. Merge branch 'cansav09/snv-add-eval' into snv-comparison

    Candace Savonen committed Oct 9, 2019
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  11. Add initial comparison notebook

    Candace Savonen committed Oct 9, 2019
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Commits on Oct 17, 2019

  1. Notebook adjustments

    Candace Savonen committed Oct 17, 2019
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  2. Fixed dumb label mix-up problem

    Candace Savonen committed Oct 17, 2019
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  3. Further honing things

    Candace Savonen committed Oct 17, 2019
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Commits on Oct 18, 2019

  1. Added the other plots except that one combo plot

    Candace Savonen committed Oct 18, 2019
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  2. Add rendered version too

    Candace Savonen committed Oct 18, 2019
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  3. Rough draft of all plots here

    Candace Savonen committed Oct 18, 2019
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  4. Get rid of upsettR's blank plot

    Candace Savonen committed Oct 18, 2019
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  5. Refresh the notebook

    Candace Savonen committed Oct 18, 2019
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  6. Run linter

    Candace Savonen committed Oct 18, 2019
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  7. Merge remote-tracking branch 'origin/snv-comparison' into snv-comparison

    Candace Savonen committed Oct 18, 2019
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  8. Change name to reflect the data better

    Candace Savonen committed Oct 18, 2019
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  9. Add to CircleCI and Dockerfile

    Candace Savonen committed Oct 18, 2019
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  10. Merge branch 'master' into snv-comparison

    @cansavvy
    cansavvy authored Oct 18, 2019
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  11. Try to fix busted CircleCI command

    Candace Savonen committed Oct 18, 2019
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  12. Merge remote-tracking branch 'origin/snv-comparison' into snv-comparison

    Candace Savonen committed Oct 18, 2019
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  13. Attempt to fix Dockerfile build problem

    Candace Savonen committed Oct 18, 2019
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Commits on Oct 21, 2019

  1. Attempt to fix docker build

    Candace Savonen committed Oct 21, 2019
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  2. Some Docker probs fixed

    Candace Savonen committed Oct 21, 2019
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  3. Push latest notebook and Dockerfile

    Candace Savonen committed Oct 21, 2019
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  4. Dockerfile appears to be building right.

    Candace Savonen committed Oct 21, 2019
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  5. Couple more things to finish up Dockerfile adds

    Candace Savonen committed Oct 21, 2019
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  6. development thing was left

    Candace Savonen committed Oct 21, 2019
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Commits on Oct 22, 2019

  1. Add Template for results discussion

    Candace Savonen committed Oct 22, 2019
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  2. Updates to notebook. Function and etc.

    Candace Savonen committed Oct 22, 2019
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  3. Refresh notebook

    Candace Savonen committed Oct 22, 2019
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  4. Add png saves to each plot

    Candace Savonen committed Oct 22, 2019
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  5. Added options to calculate_vaf_tmb.R script

    Candace Savonen committed Oct 22, 2019
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  6. Add set up for vaf_filter experiment

    Candace Savonen committed Oct 22, 2019
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Commits on Oct 23, 2019

  1. Push separate notebook for vaf_filter exp

    Candace Savonen committed Oct 23, 2019
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  2. Changes to README

    Candace Savonen committed Oct 23, 2019
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  3. Merge branch 'master' into snv-comparison

    @cansavvy
    cansavvy authored Oct 23, 2019
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  4. Add more documentation

    Candace Savonen committed Oct 23, 2019
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  5. Push VAF cutoff experiment notebook

    Candace Savonen committed Oct 23, 2019
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  6. Update title of vaf notebook

    Candace Savonen committed Oct 23, 2019
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  7. Update notebook

    Candace Savonen committed Oct 23, 2019
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  8. Fix path problem and also extend no_region option

    Candace Savonen committed Oct 23, 2019
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  9. Merge remote-tracking branch 'upstream/master' into snv-comparison

    Candace Savonen committed Oct 23, 2019
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  10. Fix typo

    Candace Savonen committed Oct 23, 2019
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  11. Added some documentation

    Candace Savonen committed Oct 23, 2019
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  12. Prep consensus mutation file saving

    Candace Savonen committed Oct 23, 2019
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Commits on Oct 24, 2019

  1. Merge remote-tracking branch 'upstream/master' into snv-comparison

    Candace Savonen committed Oct 24, 2019
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  2. Fix sex chr mislabeling in COSMIC file per @jashapiro 's suggestion

    Candace Savonen committed Oct 24, 2019
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  3. Get rid of regional analysis. Linter the notebooks Add changes to plots

    Candace Savonen committed Oct 24, 2019
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  4. Updated COSMIC file

    Candace Savonen committed Oct 24, 2019
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Commits on Oct 25, 2019

  1. Streamline this branch

    Candace Savonen committed Oct 25, 2019
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  2. Revert unneeded changes

    Candace Savonen committed Oct 25, 2019
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  3. Clean up README

    Candace Savonen committed Oct 25, 2019
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  4. Add --no_region option to README

    Candace Savonen committed Oct 25, 2019
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  5. Merge branch 'snv-caller_revamp' into vaf_filter_experiment

    Candace Savonen committed Oct 25, 2019
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  6. Refresh notebook

    Candace Savonen committed Oct 25, 2019
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  7. Add these packages to the Dockerfile

    Candace Savonen committed Oct 25, 2019
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  8. Merge remote-tracking branch 'jaclyn-taroni/master' into snv-caller_r… 

    …evamp
    Candace Savonen committed Oct 25, 2019
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  9. Merge remote-tracking branch 'jaclyn-taroni/master' into vaf_filter_e… 

    …xperiment
    Candace Savonen committed Oct 25, 2019
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  10. Fix Dockerfile dup problem

    Candace Savonen committed Oct 25, 2019
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  11. Get rid of dumb spaces

    Candace Savonen committed Oct 25, 2019
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  12. edit readme remnant

    Candace Savonen committed Oct 25, 2019
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  13. Push factor re-level change

    Candace Savonen committed Oct 25, 2019
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  14. Add to CircleCI

    Candace Savonen committed Oct 25, 2019
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  15. refresh R notebook

    Candace Savonen committed Oct 25, 2019
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  16. Merge remote-tracking branch 'upstream/master' into snv-caller_revamp

    Candace Savonen committed Oct 25, 2019
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  17. Make saving to RDS an option

    Candace Savonen committed Oct 25, 2019
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  18. Add rds saving

    Candace Savonen committed Oct 25, 2019
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  19. Rid of dev remnant

    Candace Savonen committed Oct 25, 2019
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  20. Merge remote-tracking branch 'upstream/master' into vaf_filter_experi… 

    …ment
    Candace Savonen committed Oct 25, 2019
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  21. Merge remote-tracking branch 'upstream/master' into vaf_filter_experi… 

    …ment
    Candace Savonen committed Oct 25, 2019
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  22. Fix CircleCI to be it's own test for this

    Candace Savonen committed Oct 25, 2019
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  23. Tidy up spacing

    Candace Savonen committed Oct 25, 2019
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  24. Move "Add your analysis here" to where it was supposed to be

    Candace Savonen committed Oct 25, 2019
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  25. Get rid of error causing indent

    Candace Savonen committed Oct 25, 2019
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  26. Update docs

    Candace Savonen committed Oct 25, 2019
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  27. Merge branch 'master' into rds_option_snv

    @cansavvy
    cansavvy authored Oct 25, 2019
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  28. Get rid of some things that are not needed

    Candace Savonen committed Oct 25, 2019
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  29. Make README more parallel to this change

    Candace Savonen committed Oct 25, 2019
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  30. Neaten up the nb

    Candace Savonen committed Oct 25, 2019
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  31. switch tsv/rds logic for 01-calc to reflect default

    Candace Savonen committed Oct 25, 2019
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  32. Make region file also save to RDS

    Candace Savonen committed Oct 25, 2019
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  33. change to warnings and then default to rds

    Candace Savonen committed Oct 25, 2019
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Commits on Oct 28, 2019

  1. Merge branch 'rds_option_snv' into vaf_filter_experiment

    Candace Savonen committed Oct 28, 2019
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  2. Change notebook to RDS

    Candace Savonen committed Oct 28, 2019
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  3. Have notebook call script to create vaf files

    Candace Savonen committed Oct 28, 2019
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  4. Set ggpairs' cardinality_threshold setting to NULL

    Candace Savonen committed Oct 28, 2019
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  5. Upgroup data.frame so function works again

    Candace Savonen committed Oct 28, 2019
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  6. Try to fix plot saving error

    Candace Savonen committed Oct 28, 2019
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  7. Forget about saving those plots

    Candace Savonen committed Oct 28, 2019
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  8. Merge remote-tracking branch 'upstream/master' into vaf_filter_experi… 

    …ment
    Candace Savonen committed Oct 28, 2019
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  9. Run through linter

    Candace Savonen committed Oct 28, 2019
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  10. Update html and fix dir ref

    Candace Savonen committed Oct 28, 2019
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  11. Change comment.

    Candace Savonen committed Oct 28, 2019
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  12. Show the name of the bash script

    Candace Savonen committed Oct 28, 2019
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Commits on Oct 29, 2019

  1. Get rid of sample variance section and refresh notebook

    Candace Savonen committed Oct 29, 2019
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  2. Merge branch 'master' into vaf_filter_experiment

    @cansavvy
    cansavvy authored Oct 29, 2019
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