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COOLER(1) User Commands COOLER(1)

NAME

cooler - sparse, compressed, binary persistent storage

SYNOPSIS

cooler [OPTIONS] COMMAND [ARGS]...

DESCRIPTION

Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.

The cooler file format is an implementation of a genomic matrix data model using HDF5 as the container format. The cooler package includes a suite of command line tools and a Python API to facilitate creating, querying and manipulating cooler files.

OPTIONS

Verbose logging.
On error, drop into the post-mortem debugger shell.
Show the version and exit.
Show this message and exit.

Commands:

Create a cooler from genomic pairs and bins.
Create a cooler from a pre-binned matrix.
Merge multiple coolers with identical axes.
Coarsen a cooler to a lower resolution.
Generate a multi-resolution cooler file by coarsening.
Out-of-core matrix balancing.
Display a cooler's info and metadata.
Dump a cooler's data to a text stream.
Display and browse a cooler in matplotlib.
Generate fixed-width genomic bins.
Generate fragment-delimited genomic bins.
Sort and index a contact list.
List all coolers inside a file.
Copy a cooler from one file to another or within the same file.
Create a hard link to a cooler (rather than a true copy) in the...
Rename a cooler within the same file.
Display a file's data hierarchy.
Display a file's attribute hierarchy.

AUTHOR


This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.

June 2020 cooler 0.8.7