• Add cell lines sub-selection

• Allow to select all options at once

Alignment statistics should be save in a results sub-directory, such as results/{token}/bowtie2/statistics.txt.

• Save statistics in a text file

• If the "non-genes" mode is activated and no BED annotation file is loaded, the application will not run.

Replace Jupyter Lab automatic opening with Jupyter Notebook after PitViper execution when using GUI.

Add bowtie2=2.2.4 and samtools=1.14 to env.

To do:

• Preset options:

--very-fast
Same as: -D 5 -R 1 -N 0 -L 25 -i S,1,2.00

--fast
Same as: -D 10 -R 2 -N 0 -L 22 -i S,1,1.75

--sensitive
Same as: -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default in --local mode)

--very-sensitive
Same as: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

Min. reads cut-off in GUI.

Remove:

and

Move in GUI:

A refactoring of the previous script is necessary to make the purpose of the script clear.

• Add docstrings
• Add a main function
• Remove unused functions
• Threshold from GUI/config

Add a check button for union selection instead of default intersection in integration module.

Allow user to give as input a BED file for automatic annotation of targeted elements, i.e. super-enhancers.

• Ratio_of_Classes
• Signal2Noise (default, if number of replicates >= 3)

To improve the function, we could use Python's subprocess library to execute the command instead of using os.system to run the command. This would allow us to access the output of the command and take action based on it. Additionally, we could use string formatters to make the command string more readable and easier to debug. Here is an example of how the function could be improved:

import subprocess

def run_pitviper(configfile, dry_run, jobs, notebook):
    if notebook != "":
        nb_opt = f"--edit-notebook {notebook}"
    else:
        nb_opt = ""
    if dry_run:
        cmd = f"snakemake -s workflow/Snakefile -n --configfile {configfile} --use-conda --cores {jobs}"
    elif not dry_run:
        cmd = f"snakemake -s workflow/Snakefile --configfile {configfile} --use-conda --cores {jobs} {nb_opt}"
    print("Command:", cmd)
    result = subprocess.run(cmd, shell=True, capture_output=True)
    if result.returncode == 0:
        # command succeeded
    else:
        # command failed

• Use subprocess instead of os.system

• Check if a result directory already exists for a given token. If yes, automatically add a numerical suffix to it.

• Change fold-change to RRA score
• Display two plots for MAGeCK-RRA

To do:

• Use raw counts for RRA and MLE
• Add normalization option to RRA
• Review the normalization process
• Remove normalization option of MAGeCK counts

Improve CLI options

• remove --run_snakemake, useless.

Our script seems to add a column in the design matrix that is not useful.

• Add fold-change information to BAGEL output.

Improve visualization by:

• Compute, display and link the mean normalized read counts of replicates per time-points
• Display all individual points
• Show normalization method

Add description and explanations of how to use jupyter notebbok report and export to HTML.

Let users define negatives controls in GUI.

Add (MM10,MM9,MM8,HG18,HG19,HG38) to GUI.

Add an option to choose between "per cell line" or "per primary tissue" for depmap mutations heatmap.

Validate form in GUI.

Example: SFPQ gene return an error when using show_sgRNA_counts(token):

ValueError: The condensed distance matrix must contain only finite values.

Should add a non-zero value to all cells before using Clustergrammer2.

• Check if report is created, if not display a 'failure' page to explain why.

Add cut-off in GUI for IH method

Should be possible to enter multiple elements separated a comma in TextInput widgets.

Extensibility was one of the primary goal of PitViper. However, the current implementation of the report make it very difficult and tedious to add new tools.

We should think to a manner to generalize how all functions are used.

Creating a tool agnostic class as a common interface for all results could be a solution. This class should have several characteristics:

• Generalization: should work with different results and metrics, such as FDR, Bayesian Factor or any others uncertainty measures.
• Common interface: the API should be consistent across all methods.

To create a new method, two features are mandatory: the name of the elements and at least one numerical score to rank the value (FDR, Bayesian Factor, etc.)

Find a better and more representative name for "in-house method". Then rename it in all scripts... :(

Some references are missing in GUI and report.

Use depmap_release() from http://bioconductor.org/packages/release/data/experiment/manuals/depmap/man/depmap.pdf to get data version and use it in file name to check if user have the last version.

"in-house" method default cut-off is different between modules in report.