table of contents
| 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¶
- -v, --verbose
- Verbose logging.
- -d, --debug
- On error, drop into the post-mortem debugger shell.
- -V, --version
- Show the version and exit.
- -h, --help
- Show this message and exit.
Commands:¶
- cload
- Create a cooler from genomic pairs and bins.
- load
- Create a cooler from a pre-binned matrix.
- merge
- Merge multiple coolers with identical axes.
- coarsen
- Coarsen a cooler to a lower resolution.
- zoomify
- Generate a multi-resolution cooler file by coarsening.
- balance
- Out-of-core matrix balancing.
- info
- Display a cooler's info and metadata.
- dump
- Dump a cooler's data to a text stream.
- show
- Display and browse a cooler in matplotlib.
- makebins
- Generate fixed-width genomic bins.
- digest
- Generate fragment-delimited genomic bins.
- csort
- Sort and index a contact list.
- ls
- List all coolers inside a file.
- cp
- Copy a cooler from one file to another or within the same file.
- ln
- Create a hard link to a cooler (rather than a true copy) in the...
- mv
- Rename a cooler within the same file.
- tree
- Display a file's data hierarchy.
- attrs
- 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 |