repDNA-1.1.4.zip -- The source Zip file for installing the repDNA package on Windows, Linux, Unix, Mac OS
Quick to start
repDNA_manual.pdf for how to use repDNA, and the descriptions of the 15 features in the package.
repDNA_example.pdf includes some examples of how to construct computational predictors for three tasks in computational genomics by using repDNA.
Datasets and Python scripts used in the three examples in Online Supporting Information S2 (repDNA_example.pdf)
| Tasks | Positive dataset | Negative dataset | Python script |
|---|---|---|---|
| DNasel HS prediction | hs.fasta | non-hs.fasta | example1.py |
| Nucleosome positioning prediction | H_sapiens_pos.fasta | H_sapiens_neg.fasta | example2.py |
| Recombination spot identification | hotspots.fasta | coldspots.fasta | example3.py |
| repDNA_example.zip contains all the files shown in this table. | |||
Values of the physicochemical indices
38_dinucleotide_physicochemical_indices.zip
-- the 38 physicochemical indices for dinucleotides shown in Table 1 in Online Supporting Information S1.
12_trinucleotide_physicochemical_indices.zip
-- the 12 physicochemical indices for trinucleotides shown in Table 2 in Online Supporting Information S1.
6_dinucleotide_physicochemical_indices.zip
-- the 6 physicochemical indices for dinucleotides shown in Table 3 in Online Supporting Information S1.
