The mission of enclone is to:
Find and display the clonotypes within single cell VDJ datasets:
groups of cells having the same fully rearranged common ancestor.
enclone is part of the 10x Genomics immune profiling tools, including Cell Ranger and Loupe.
enclone uses output from Cell Ranger version ≥ 3.1.
The complete enclone documentation is at bit.ly/enclone. This page catalogs the subset of those
pages that are directly accessible from the enclone command line. These pages can be viewed in a
100 wide x 56 high window, except for those labeled "long" or "wide".
┌─────────────────────────┬─────────────────────────────────────────────────────────────────────┐
│command │ what it provides │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help │ help to test for correct setup │
│enclone │ what you see here: guide to all the doc │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help quick │ quick guide to getting started │
│enclone help how │ how enclone works (long) │
│enclone help command │ info about enclone command line argument processing │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help glossary │ glossary of terms used by enclone, and conventions │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help example1 │ explanation of an example │
│enclone help example2 │ example showing gene expression and feature barcodes (wide) │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help input │ how to provide input to enclone (long) │
│enclone help input_tech │ how to provide input to enclone (technical notes) │
│enclone help parseable │ parseable output (long) │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help filter │ clonotype filtering options, scanning for feature enrichment (long)│
│enclone help special │ special filtering options (long) │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help lvars │ lead column options (long) │
│enclone help cvars │ per chain column options (long) │
│enclone help amino │ per chain column options for amino acids │
│enclone help display │ other clonotype display options (long) │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help indels │ insertion and deletion handling │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help color │ how enclone uses color, and related things │
│enclone help faq │ frequently asked questions (long) │
├─────────────────────────┼─────────────────────────────────────────────────────────────────────┤
│enclone help all │ concatenation of all the help pages (long, wide) │
│ │ ███ USE THIS TO SEARCH ALL THE HELP PAGES! ███ │
└─────────────────────────┴─────────────────────────────────────────────────────────────────────┘