expr Classes and tools related to expression array analysis.
gata.aligner For aligning and post processing DNA sequences using BLAST for subsequent import into GATAPlotter.
gata.geneGlyphs For representing annotation, scale bars, and generic tracks.
gata.main Main app, utility, and params for GATAPlotter. GATAPlotter menus, panels, and frames.
gata.plotter GATAPlotter primary panel, sliders, tools, and conservation panels.
igb.util Utilities for converting TiMAT results into Affymetrix IGB visualizations.
meme Wrapper for meme tweaked for processing multiple rounds of SELEX oligos.
selex For processing of raw SELEX sequence data.
trans.anno For associating intervals, binding regions, and binding peaks with GFF annotation.
trans.bkgrnd For examining background GC content and ratio bias.
trans.cel Apps and methods for manipulating cel files. For graphically representing '.cel' files and intervals.
trans.main Principle classes and scripts used in TiMAT2 analysis.
trans.misc Rough working scripts.
trans.qc Quality control apps for cel files.
trans.roc For manipulating the BAC dmel spike in data and generating ROC curves.
trans.tpmap For maping, filtering, and calculating statistics about text version bpmap files.  
util.apps Scripts for printing arrays, manipulating files, scatter plots... For representing gene annotation. Calculators for aligments and nucleic acids. Clustering apps and methods. Bio format converters. Restriction enzyme digestion of DNA sequences. Parsers and extractors, fasta, quality, text, gff.... GFF2 and GFF3 parsers. Nucleic acid sequence manipulation. Wrappers for other bio applications. Generation and manipulation of random sequence words of various lengths.
util.gen Variety of helper methods for Email, IO, Encryption, HTML, Swing...