Abolfazl (Abe)

New Data: data loader for cisTarget database

1

**Describe the problem** TF-target interaction is a missing opportunity as Multi-Instance Prediction. **Describe the solution you'd like** SCENIC+ / pySCENIC already has a well described resource https://resources.aertslab.org/cistarget/databases/ **Additional context** This...

ENCODE downloader

2

### Request type New module ### Request description It would be cool to have a module as `gget ENCODE`, similar to https://github.com/kundajelab/ENCODE_downloader. ### Example command https://github.com/kundajelab/ENCODE_downloader/?tab=readme-ov-file#examples ### Example return value...

### Request type New module ### Request description bioRxiv: [**Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures**](https://www.biorxiv.org/content/10.1101/2024.01.02.573913v1.full) Portal: https://g2p.broadinstitute.org/...

Implement methods for phenotype calculation and statistical analysis

1

**`preprocessing`** - [x] Implement function to add pseudocounts **`phenoscore`** - [x] #25 - [x] #71 - [x] #80 - [x] #85 - [x] #17 - [x] #87 - [x] #16...

Functions to build data dashboard and interactive plots

1

- [x] draft a module called `dashboard` - [ ] comment codes and include this module in the ReadTheDocs files **Plots related to #20** - [x] rho volcano plot -...

Add a section for background and references

1

- [x] Name research articles used to develop ScreenPro2 - [ ] Describe what concepts used from each paper - [ ] Link to related and useful review papers for...

### 1. How to process raw FASTQ files using ScreenPro2's NGS module - [x] toy FASTQ files for single-guide and dual-guide design ___ ### 2. How to calculate phenotypes using...

Functions for common QC and phenotype level plots

1

- [x] transfer codes from https://github.com/mhorlbeck/ScreenProcessing/blob/master/screen_analysis.py **QC plots** - [x] #22 - [ ] Histogram of guide counts distribution - [ ] PCA plot - [x] #9 **phenotype plots** -...