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Lancet exploration notebook series: Part 1 TCGA-PBTA comparison variations #557

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Mar 6, 2020
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Lancet exploration notebook series: Part 1 TCGA-PBTA comparison variations #557

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b84db10
Add exploration notebook
cansavvy Feb 25, 2020
315d8d3
Add to CircleCI
cansavvy Feb 25, 2020
50bd252
update gitiugnore to include a file for this analysis
cansavvy Feb 25, 2020
869171b
Update notebooks
cansavvy Feb 25, 2020
6f8f56b
Add only the one ref file
cansavvy Feb 25, 2020
6b4c1ff
Fix circleCI file path
cansavvy Feb 25, 2020
e3b32f6
Update .circleci/config.yml file path
cansavvy Feb 25, 2020
63bed5f
Rearrange order of CircleCI tests
cansavvy Feb 25, 2020
86a0a92
Add better documentation
cansavvy Feb 26, 2020
b58941a
Fix date
cansavvy Feb 26, 2020
9b3c9be
Merge branch 'master' into lancet-tests-1
cansavvy Feb 27, 2020
2b46d95
Merge branch 'master' into lancet-tests-1
cansavvy Feb 28, 2020
b13e7bf
Merge remote-tracking branch 'upstream/master' into lancet-tests-1
cansavvy Feb 28, 2020
3ccd0c6
Update the notebook and plots with redone data
cansavvy Feb 29, 2020
4e08f3e
Merge remote-tracking branch 'upstream/master' into lancet-tests-1
cansavvy Feb 29, 2020
62828b7
Merge branch 'master' into lancet-tests-1
cansavvy Mar 3, 2020
90fcee9
fix file reference
cansavvy Mar 3, 2020
3b3fd1c
Merge branch 'master' into lancet-tests-1
jashapiro Mar 4, 2020
1afb5d4
Merge remote-tracking branch 'upstream/master' into lancet-tests-1
cansavvy Mar 4, 2020
0bd853c
Incorporate some @jashapiro suggestions and add more documentation ab…
cansavvy Mar 4, 2020
7e0fb4e
Merge remote-tracking branch 'origin/lancet-tests-1' into lancet-tests-1
cansavvy Mar 4, 2020
a504ca3
Fix plot rendering
cansavvy Mar 4, 2020
f5b0cb7
Merge branch 'master' into lancet-tests-1
cansavvy Mar 5, 2020
7c63ca9
Undo accidental bolding
cansavvy Mar 5, 2020
da85445
Push changes of function
cansavvy Mar 5, 2020
1a2f956
push refreshed notebook
cansavvy Mar 5, 2020
7e2f36e
change to 0, 12 substr for all samples and refresh notebook
cansavvy Mar 5, 2020
584d7fa
Merge branch 'master' into lancet-tests-1
cansavvy Mar 5, 2020
8536e84
Merge branch 'master' into lancet-tests-1
jaclyn-taroni Mar 6, 2020
17d4557
Merge branch 'master' into lancet-tests-1
jaclyn-taroni Mar 6, 2020
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3 changes: 3 additions & 0 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -167,6 +167,9 @@ jobs:
name: Telomerase activity
command: ./scripts/run_in_ci.sh bash analyses/telomerase-activity-prediction/RUN-telomerase-activity-prediction.sh

- run:
name: PBTA vs TCGA explore
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-test/explore-tcga-pbta.Rmd', clean = TRUE)"

################################
#### Add your analysis here ####
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4 changes: 3 additions & 1 deletion analyses/snv-callers/.gitignore
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@@ -1,3 +1,5 @@
# ignore folders with big results files
results
ref_files
ref_files/*
!ref_files/hg38_liftover_genome_gencode.v19.basic.exome.bed

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