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Python workflows #82

Merged
merged 89 commits into from
Jan 25, 2023
Merged

Python workflows #82

merged 89 commits into from
Jan 25, 2023

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panushri25
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@panushri25
modisco-lite-integration
4a8ed65
@panushri25
removing logs from main, only keeping in branch
0ae25d8
@panushri25
integrating automatic shift detection scripts
e956291
@panushri25
updating docker with the bioconda pybigwig fix
8df9590
@panushri25
removed warning and changed data type to ATAC and DNASE
12a60b3
@panushri25
added data directory files
a32fa70
@panushri25
fixed indirect import for meme and some file naming
ebe8a06
@panushri25
removed warning and added tomtom installation
cc7f068
@panushri25
added pdf output for modisco reports
5f9e476
@panushri25
changed ATAC_PE to ATAC
c9ffd95
@panushri25
shift only end when + and start when - on strand, prevents negative v…
37e1de7 
…alue errors in bedgraph
@panushri25
remove print statements
727684d
@panushri25
adding chrombpnet_makebigwig output to logs
f79a708
@panushri25
changing tutorial directory
72e7d8c
@panushri25
changing chrombpnet_wo_bias.h5 to chrombpnet_nobias.h5
567ea74
@panushri25
changing chrombpnet_wo_bias.h5 to chrombpnet_nobias.h5
a8ab3a2
@panushri25
fixing typos
44672c4
@panushri25
added flags for input and fixed type in step 6
95683fc
@panushri25
moved tutorial to a different folder
6054e2d
@panushri25
updated shorted readme
73d012d
@panushri25
testing model pdf display
786bccf
@panushri25
new pdf chrombpnet image
0f08aa9
@panushri25
README update, fix syntax in train_chrombpnet workflow script, add co…
6c204ad 
…mmand line to generate contribution score bigwigs
@panushri25
Added outline for two main workflow commands in README
07173ee 
Added outline for two main work flow commands in README
@panushri25
Added hyperlinks to input file formats
b4c8778 
Added hyperlinks to input file formats
@panushri25
hyperlink fragment, tagaligns and full documentation
5a2bec8 
hyperlink fragment, tagaligns and full documentation
@panushri25
workflow to input fragment and tagaligns too
c7c9adc
@panushri25
Documentation for bias model training added
10334ae
@panushri25
png files with better names
35a0d88
@panushri25
added bias threshold factor
3009973
panushri25 and others added 27 commits December 20, 2022 08:22
@panushri25
added init file for scripting
20b75d5
@panushri25
adding metrics evaluation
5bb3f3a
@panushri25
adding script to generate splits
f8e2259
@panushri25
removing tutorial and gc matched negatives from setup
baa6eab
@panushri25
1.3 version fix
9226200
@panushri25
removed counts interpret and modisoc in the chrombpnet pipeline to re…
705eb3e 
…duce time, added shap to requirements
@panushri25
reproducible gc matching nonpeaks with seed
22bc12e
@annashcherbina
downgrading weasyprint to not require recent versions of pango
aabb4f1
@panushri25
added tn5 and dnase pwms to meme database
748eb5e
@panushri25
fixing imports for modisco reports
f1adee7
@panushri25
fixed stride to have -st
403388d
@panushri25
moved modisco html directory to evaluation
97a049e
@panushri25
updated readme with latest command
85295a2
@panushri25
added input arguments link
90d9e80
@panushri25
added input arguments link
2770d0f
@panushri25
shorted meme tn5 motifs
943264c
@panushri25
fixing tabs
56d4e07
@panushri25
removing redundant json file saving
ba71212
@panushri25
added more detailed comments in the report, added warning for bias co…
cfa0a28 
…unts pearsonr in -0.3 to -0.5 range
@panushri25
added html_prefix argument
ebb3312
@panushri25
increase bias model performance in peaks check, print statement to sh…
4a79a5f 
…ow pearsonr
@panushri25
removed findfont warnings, typos in printing, import fix
929302d
@panushri25
updated modisco lite requirement that reduces findfont error
14fdd37
@panushri25
Fixed different syntax for uncorrected
4213b22
@panushri25
added html prefixing for bias model
1c616b9
@panushri25
updating setup file
2887b56
@panushri25
updated version to base
2b3bf6e
@annashcherbina annashcherbina self-requested a review January 25, 2023 01:25
@panushri25 panushri25 merged commit 3f30813 into master Jan 25, 2023
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@annashcherbina annashcherbina annashcherbina approved these changes

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@panushri25 @annashcherbina