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- Hello tcrdist3 — tcrdist3 0. 1. 0 documentation - Read the Docs
Hello tcrdist3 ¶ tcrdist3 can be run interactively One way to get started is to try a few examples Examples use the data file (dash csv)
- TCR Distances — tcrdist3 0. 1. 0 documentation - Read the Docs
For instance, the Cython enabled packages like python-Levenshtein metrics can be used seamlessly with tcrdist3 Dictionary keys must match appropriate columns of the clone_df DataFrame
- Visualizing — tcrdist3 0. 1. 0 documentation - Read the Docs
Visualizing ¶ Some of the most popular features of the original tcrdist code were its beautiful SVG based graphics For instance, gene usage plots visualize the frequency with which different V and J genes are used within a T cell repertoire Because some users may wish to make these plots without using the other feature of tcrdist2, we have built them as stand-alone features That means if
- Working with Bulk Data — tcrdist3 0. 1. 0 documentation
For analysis of large repertoires, such as those commonly generated from bulk PMBC TCR beta chain sequencing, tcrdist3 provides the option to fragment the pairwise distance computation into chunks, storing the intermediate results to disk
- Inputs — tcrdist3 0. 1. 0 documentation - Read the Docs
Tcrdist3 only requires 3 input columns for single chain analysis (i e , for beta chain cdr3_b_aa and v_b_gene, j_b_gene) and 6 columns for paired chain analysis (i e , cdr3_b_aa, v_b_gene, j_b_gene, cdr3_a_aa, v_a_gene, and j_a_gene) More columns can be included depending on the application
- (Quasi)Public Clones — tcrdist3 0. 1. 0 documentation
tcrdist3 has a memory efficient options for larger datasets that produce scipy sparse rather than dense representations of distance relationships Currently you can’t call TCRpublic () on this sparse representation
- CDR3 Motifs — tcrdist3 0. 1. 0 documentation - Read the Docs
This example introduces features that are implemented in two stand-alone pip installable python pakcages, by tcrdist3’s authors, tcrsampler and palmotif They are more extensively documented on their own project pages, but we introduce their use here with some basic illustrative examples in the Modules section of this page
- Tabulating Meta-Clonotypes — tcrdist3 0. 1. 0 documentation
import multiprocessing import numpy as np import os import pandas as pd from tcrdist setup_tests import download_and_extract_zip_file from tcrdist repertoire import TCRrep from tcrdist breadth import get_safe_chunk from tcrdist join import join_by_dist import re ncpus = min(multiprocessing cpu_count(), 6) files = ['1588BW_20200417_PBMC_unsorted
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