cooler1
Sparse, compressed, binary persistent storage
Usage
cooler [OPTIONS]
COMMAND
[ARGS] ...
Overview
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. |
Releases
Unchanged in 2 releases since Debian 12 (Bookworm).