Packages

nix.affy.anno	For associating intervals, binding regions, and binding peaks with GFF annotation.
nix.affy.bkgrnd	For examining background GC content and ratio bias.
nix.affy.bpmap	For maping, filtering, and calculating statistics about text version bpmap files.
nix.affy.graphics	For graphically representing '.cel' files and intervals.
nix.affy.main	Principle classes and scripts used in TiMAT analysis.
nix.affy.misc	Rough working scripts.
nix.affy.roc	For manipulating the BAC dmel spike in data and generating ROC curves.
nix.bdtnp.bid	Bio Imaging Database, 2nd pass, see Lisa's code for latest version.
nix.gata.aligner	For aligning and post processing DNA sequences using BLAST for subsequent import into GATAPlotter.
nix.gata.geneGlyphs	For representing annotation, scale bars, and generic tracks.
nix.gata.main	Main app, utility, and params for GATAPlotter.
nix.gata.menu	GATAPlotter menus, panels, and frames.
nix.gata.plotter	GATAPlotter primary panel, sliders, tools, and conservation panels.
nix.meme	Wrapper for meme tweaked for processing multiple rounds of SELEX oligos.
nix.selex	For processing of raw SELEX sequence data.
nix.util.apps	Scripts for printing arrays, manipulating files, scatter plots...
nix.util.bio.annotation	For representing gene annotation.
nix.util.bio.calc	Calculators for aligments and nucleic acids.
nix.util.bio.converters	Bio format converters.
nix.util.bio.digest	Restriction enzyme digestion of DNA sequences.
nix.util.bio.parsers	Parsers and extractors, fasta, quality, text, gff....
nix.util.bio.parsers.gff	GFF2 and GFF3 parsers.
nix.util.bio.seq	Nucleic acid sequence manipulation.
nix.util.bio.wrappers	Wrappers for other bio applications.
nix.util.bio.xamer	Generation and manipulation of random sequence words of various lengths.
nix.util.gen	Variety of helper methods for Email, IO, Encryption, HTML, Swing...
nix.xml	Xml manipulation.