Available Modules

clue_api_client

A Python client for easy interaction with the Connectivity Map (CLUE) API.

Maintainer: David Lahr, dlahr@broadinstitute.org

pandasGEXpress

A package (integrated with Python’s pandas package) allowing users to easily read, modify, and write .gct and .gctx files.

Also features the following command-line tools:

gct2gctx: converts .gct to .gctx file. Type gct2gctx -h for help.

gctx2gct: converts .gctx to .gct file. Type gctx2gct -h for help.

concat: Concats two or more .gct/x files as specified by user. Type concat -h for help.

Maintainer: Oana Enache, oana@broadinstitute.org

set_io

set_io contains simple scripts for parsing two other common file types used by the Connectivity Map: GRP and GMT files. The GRP file is used for storing a single set of things (e.g. a single gene set), while the GMT file is used for storing multiple sets of things (e.g. several gene sets).

Maintainer: Lev Litichevskiy, lev@broadinstitute.org