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Packages |
| bioroot |
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| bioroot.antibody |
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| bioroot.oligo |
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| bioroot.parsers |
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| bioroot.plasmid |
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| bioroot.strain |
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| cgar |
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| com.amazon.s3 |
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| com.amazon.thirdparty |
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| 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. |
| gata.menu |
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. |
| trans.graphics |
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.amazon |
|
| util.apps |
Scripts for printing arrays, manipulating files, scatter plots... |
| util.bio.annotation |
For representing gene annotation. |
| util.bio.calc |
Calculators for aligments and nucleic acids. |
| util.bio.cluster |
Clustering apps and methods. |
| util.bio.converters |
Bio format converters. |
| util.bio.digest |
Restriction enzyme digestion of DNA sequences. |
| util.bio.parsers |
Parsers and extractors, fasta, quality, text, gff.... |
| util.bio.parsers.gff |
GFF2 and GFF3 parsers. |
| util.bio.seq |
Nucleic acid sequence manipulation. |
| util.bio.wrappers |
Wrappers for other bio applications. |
| util.bio.xamer |
Generation and manipulation of random sequence words of various lengths. |
| util.gen |
Variety of helper methods for Email, IO, Encryption, HTML, Swing... |
| util.xml |
|