Remove the silencing column and provide a Python script for computing it
Created by: arteymix
There's a lot of work coming in for improving the silencing metric and it will likely not involve a C implementation due to the complexity of the statistical models involved.
-
remove CDS extraction and use exclusively Biopython? (likely inefficient) -
compute miRNA-induced silencing -
compute target silencing
To resume the implementation requirements:
- use Poisson-Binomial distribution for ponderating the scores for different number of adjuvant miRNAs (implementation https://github.com/tsakim/poibin) into individual miRNA-induced silencing
- use the formulae for measuring the silencing on the target knowning independent and linear site silencing
The script should be capable of reading a single experiment in detailed mode and multiple experiments in target summary mode. One could use it for computing and aggregating the silencing on many experiments in a single operation.
mirbooking-compute-silencing
[--summary]
[--cds-regions]
[--3prime-multiplier]
[--5prime-multiplier]
[--cds-multiplier]
[--output=FILE]
<experiments>
--target-summary