Routines for Import |
Executable |
File |
Description |

| X | GetDataFiles.py | Download support data files and routines over the internet. |

X | | HT.py | Load/Encapsulate/Slice High-throughput (genome-scale) datasets |

X | X | MotifMetrics.py | Compute motif overrepresentation statistics among a sequence set, as compared to all sequences in a genome. Search of highest scoring k-mer motifs. |

X | | MotifTools.py | Kitchen-sink motif object |

| X | Sitemap.py | Print ascii-maps of motif occurence among sets of sequences |

X | | DataSources/GO.py | Interface to Gene Ontologies, including statistical tests. |

X | | DataSources/Holstege.py | Interface to expression rate data from Holstege et. al. |

X | | DataSources/Novartis.py | Interface to GeneAtlas. |

X | | DataSources/PDB.py | A very simple PDB parser for 3-D protien/DNA structures |

X | | DataSources/SGD.py | Interface to the SGD yeast database, including genomic sequence. |

X | | DataSources/Yeast6kArray.py | Interface to the 6k intergenic array, including mappings from probes to genomic features. |

X | | Clustering/Kmedoids.py | K-medoids algorithms for motif clustering. |

X | | Clustering/MotifCompare.py | Utility routines for aligning and comparing motifs |

X | X | Clustering/UPGMA.py | UPGMA algorithm for motif clustering. |

X | | MD/EM.py | Interface to C++ routines for MD via Expectation Maximization |

X | | MD/MDsupport.py | Wrapper for motif-related C++ routines |

X | X | MD/MDscan.py | Interface to MDscan program. |

X | X | MD/AlignAce.py | Interface to the AlignACE program. |

X | X | MD/Meme.py | Interface to the MEME program. |

X | X | MD/TAMO_EM.py | TAMO's very own EM implementation, that allows careful control over the seeds used for search. |

| X | MDconvert/ace2tamo.py | Motif File Format Conversion Programs.
The TAMO format is described here. |

| X | MDconvert/kellis2tamo.py | |

| X | MDconvert/meme2tamo.py | |

| X | MDconvert/memeset2tamo.py | |

| X | MDconvert/tamo2table.py | |

| X | MDconvert/tamo2tamo.py | |

X | | localpaths.py | Path information for TAMO |

X | | paths.py | More Path information for TAMO |

| X | seq/Background.py | Compute high-order Markov background model from a collection of sequences. |

X | | seq/FakeFasta.py | Generate, seed, and randomly select sequences (for statistical testing.) |

X | | seq/Fasta.py | Fast Fasta IO |

| X | seq/GenerateFastas.py | Generate a collection of sequence files from genome-wide data and sequence. |

X | | seq/Human.py | Fast, random-access interface to human sequence. |

X | | util/Arith.py | Several very useful arithmetic routines and statistical test (hypergeometric & bionomial) |

X | | util/PermuteTools.py | Routines for generating sequence permutations of k-mers. Useful for coarse-grained motif search (if fused with MotifMetrics.py) |

X | | util/Poisson.py | Poisson statistical tests and fitting routines to Poisson distributions |

X | | util/WMWtest.py | Wilcoxon / Mann-Whitney rank sum test |

X | | util/swilk.py | Shapiro-Wilk normality test (interfaces to underlying C++ routine) |