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update: cosmetic changes in quantification scripts #110

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wants to merge 32 commits into from
Closed

update: cosmetic changes in quantification scripts #110

wants to merge 32 commits into from

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lschaerfen
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Changes suggested by @dominikburri

Checklist

  • I have performed a self-review of my own code
  • My code follows the templates/style guidelines of the repository
  • I have commented my code, particularly in hard-to-understand areas
  • I have tested my code

lschaerfen and others added 29 commits May 27, 2021 10:31
@lschaerfen
Q3: annotating PAS, calculating per-gene usage
6bafc67
different input files, ideas to map PAS between different data sets
6503f35
@lschaerfen
added some commentary, separate files (separate from the jupyter note…
ef1fdfe 
…book) to run the PAS annotation
@lschaerfen
adding annotation bed for mouse
ff0fa7d
@yuukiiwa
add dockerized QAPA execution workflow with quantification bed
61ec562
@lschaerfen
adding script for ground truth matching
a0f22c5
fixed bug in file naming
4a82dcf
added script to calculate correlation coefficient between prediction …
4c14a4e 
…and ground truth quantification
updated
09e8d98
updated
96d605f
@yuukiiwa
use apaeval/qapa:1.3.1
84d432a
@yuukiiwa
update summary workflows based on the latest updates in the TCGA example
8f9d647
@yuukiiwa
Merge branch 'iRNA-COSI:main' into main
7964397
@yuukiiwa
add Q2 summary workflow
38c83a7
@lschaerfen
named columns to increase readability
6cf98e7
@lschaerfen
removed merging predicted sites, added non-matched files to the outpu…
f641e8c 
…t, removed handling one predicted site matching with multiple ground truth sites for now (these sites are discarded)
@yuukiiwa
step 1 and 3 are now running on docker, figuring how to dockerize step 2
90ceb52
@yuukiiwa
update metrics docker container
9fd5be2
@yuukiiwa
Q2 summary workflow running with Leo quantification metrics scripts
319286c
@yuukiiwa
Merge pull request iRNA-COSI#2 from lschaerfen/main
3ac271b 
get original metrics calculation scripts from Leo
@yuukiiwa
add original metric calculation scripts from Leo fork
4ea5ba4
@yuukiiwa
Merge branch 'iRNA-COSI:main' into main
f77a2f7
@yuukiiwa
Update check_samplesheet.nf
2399ec1
@yuukiiwa
Update make_differential_tsv.nf
35e7f24
@yuukiiwa
Update make_quant_bed.nf
ce8c987
@yuukiiwa
Update check_samplesheet.nf
30d956b
@yuukiiwa
Update make_quant_bed.nf
4ec464f
@lschaerfen
Merge branch 'iRNA-COSI:main' into main
571bf56
@lschaerfen
added option for output file name, increased readability, cosmetic ch…
4e3b74c 
…anges
mzavolan
mzavolan reviewed Jun 3, 2021
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Looks good!

mzavolan
mzavolan previously approved these changes Jun 3, 2021
View reviewed changes
@lschaerfen
Merge pull request #1 from yuukiiwa/main
d32d734 
for updating metric calculation
@lschaerfen lschaerfen closed this Jun 3, 2021
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@lschaerfen @mzavolan @dominikburri @yuukiiwa