This repository is a shared resource created by the Computational Biology and Informatics Laboratory (CBIL) in Penn’s Institute for Biomedical Informatics. It contains a variety of scripts and packages for bioinformatics applications and other general purpose code.

• yarn / npm / ant
• environment variables for GUS_HOME and PROJECT_HOME
• Internal Dependencies
  • install

• bld CBIL

Bio

library of value objects for biologically meaningful entities and file types. deprecated in favor of Bioperl.

Cider

set of packages that help generate a website with using page body parts, a navbar, and a configurable look-and-feel.

CSP

CBIL Style Police (CSP) is a Perl package for generating HTML pages and forms in a principled manner.

HQ

library of value objects used when computing hierarchical entropy values

ISA

readers and library of value objects for ISA-Tab Format

TranscriptExpression

Modules for analyzing expression data (Microarray and RNASeq) and other data types.

Util

Helper modules for a variety of tasks