pepbox 0.3.8
Peptide specific TCR identification based on expansion.

pepbox
======

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T cell activation that leads to a productive T-cell reaction against a
pathogen agent is linked to its T cell receptor (TCR) specificity. The
ability of the TCR to distinguish between structurally unrelated to
similar peptides defines the T cell specificity. The affinity drives the
specifcity. A T cell that binds to peptide-MHC complex with enough
affinity will increase the magnitude of the immune response (i.e. T cell
expansion). Therefore, expansion is a powerful feature to measure TCRs
specifity. This application has the goal to quantify if T cell
clonotypes (i.e. group of T cells sharing the same TCR) are
significantly expanded by comparing their respective frequency before
and after contact with a peptide. To improve performance of peptide
specific clonotypes selection, irrelevant peptide stimulated cultured T
cells or/and medium cultured T cells can be provided as negative
controls. A list of reference TCRs known to be specific to the relevant
peptide (e.g. obtained from tetramer staining, IFNg capture) are used to
define optimal expansion thresholds for selecting positively and
negatively expanded T cells

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Parameters
==========

usage:
------

pepbox.py [-h] [-merge] [-expansion] [-analyze] [-reproducibility]
[-aacdr3] [-genes_cdr3_aacln] [-optimize] [-timepoints] [-geneusage]
[-detailed] [-input_folder INPUT_FOLDER] [-output_folder OUTPUT_FOLDER]
[-workdir WORKDIR] [-nolog] [-compress] [-v] [–version] [-debug]

optional arguments:
-------------------

-  -h, –help show this help message and exit
-  -merge Merge Adaptive Biotechnologies TCR sequencing txt file
   (default: False)
-  -expansion Calculate expansion p-values using a Fisher exact test
   (default: False)
-  -analyze Produce basic statistics summary tables and figures
   (default: False)
-  -reproducibility Creating heatmap of reproducibility (default: False)
-  -aacdr3 Define the clonotype at the amino acid cdr3 level (default:
   False)
-  -genes_cdr3_aacln Define the clonotype at the amino acid cdr3 and V,
   J gene level (default: False)
-  -optimize Creating negative control vs relevant peptide stimulated
   clonotype p-value plot (default: False)
-  -timepoints Analyzes samples from different time points (default:
   False)
-  -geneusage Provide gene usage statistics (default: False)
-  -detailed Provide more details
-  -input_folder INPUT_FOLDER Input folder (default: current directory)
-  -output_folder OUTPUT_FOLDER Output folder (default: current
   directory)
-  -workdir WORKDIR Folder where input and output files should be
   (default: current directory)
-  -compress Compress output folder (default: False)

-  -nolog Disable default log file (default: False)
-  -v Turns on verbosity (more details)
-  –version show program’s version number and exit
-  -debug Debug using small input size to test specific cases.

# Usage

.. code:: python

    # Merge Adaptive Biotechnologies TCR sequencing txt formatted files
    python pepbox.py -merge -workdir myworkdir
    # Common pipeline
    python pepbox.py -merge -expansion -analyze -optimize -workdir myworkdir