Commits · master · Charles / miRmap

28 Mar, 2013 3 commits
- Updates miRmap web site URL. · 7036c0de
  cev authored Mar 28, 2013
  
  7036c0de
- Updates copyright to 2013. · aa849b2e
  cev authored Mar 28, 2013
  
  aa849b2e
- Improves model selection. · 68f12cf3
  cev authored Mar 28, 2013
  
  68f12cf3
25 Mar, 2013 1 commit
- Removes prefix slope_ to parameter names of the models. · 7bbe1ce6
  cev authored Mar 26, 2013
  
  7bbe1ce6
09 Jan, 2013 1 commit
- Adds ChangeLog · 1f31eb41
  cev authored Jan 09, 2013
  
  1f31eb41
08 Jan, 2013 2 commits
- Updates documentation. · 7226adee
  cev authored Jan 08, 2013
  
  7226adee
- Small docstring fix. · 0cbf89ff
  cev authored Jan 08, 2013
  
  0cbf89ff
18 Dec, 2012 1 commit
- Adds aln_quality arg to eval_selec_phylop method. · 0a22d585
  cev authored Dec 18, 2012
  
  0a22d585
12 Dec, 2012 2 commits
- Adds the --site-id option to mirmap_runs.py. · 13587fb9
  cev authored Dec 12, 2012
  
  13587fb9
- Adds debug message for each miRNA-transcript prediction. · 0a2aba38
  cev authored Dec 12, 2012
  
  0a2aba38
07 Dec, 2012 1 commit
- Changes reduce to functools.reduce (Python 3). · 677b696a
  cev authored Dec 07, 2012
  
  677b696a
06 Dec, 2012 1 commit
- Adds combine option to mirmap_runs.py. · b0462a88
  cev authored Dec 06, 2012
  
  b0462a88
05 Dec, 2012 8 commits
- Adds score property and missing docstring in model.py. · 61e71cf3
  cev authored Dec 05, 2012
  
  61e71cf3
- Adds get_cons_bls and get_selec_phylop methods. · 0f7ea34d
  cev authored Dec 05, 2012
  
  0f7ea34d
- Adds get_prob_binomial method. · 34b3b09b
  cev authored Dec 05, 2012
  
  34b3b09b
- Small docstring fixes. · e704646a
  cev authored Dec 05, 2012
  
  e704646a
- Adds get_prob_exact method. · 07914a5c
  cev authored Dec 05, 2012
  
  07914a5c
- Adds tgs_au, tgs_position, and tgs_pairing3p properties. · f6976267
  cev authored Dec 05, 2012
  
  f6976267
- Adds dg_binding, dg_duplex_seed, and dg_binding_seed properties. Adds docstrings to thermo.py. · 4ea2928a
  cev authored Dec 05, 2012
  
  4ea2928a
- Adds multiple methods (min & exp_sum) to combine thermodynamic features. · a827c20c
  cev authored Dec 05, 2012
  
  a827c20c
12 Nov, 2012 4 commits
- Changes model selection. · aca4d6f1
  cev authored Nov 12, 2012
  
  aca4d6f1
- Adds dg_duplex_seed and dg_binding_seed features to mirmap_runs.py. · fdbb7481
  cev authored Nov 12, 2012
  
  fdbb7481
- Adds missing dg_duplex_seed and dg_binding_seed features to the final score computation. · ef4b28b9
  cev authored Nov 12, 2012
  
  ef4b28b9
- Adds new models with dg_duplex_seed and dg_binding_seed features. Cleans old models. · 1a787b65
  cev authored Nov 12, 2012
  
  1a787b65
09 Nov, 2012 4 commits
- Small fix in README.rst. · a41844fb
  cev authored Nov 09, 2012
  
  a41844fb
- Adds missing reinitialization of struc_buffer in case of no constraint folding... · 0de7ae1e
  cev authored Nov 09, 2012
```
Adds missing reinitialization of struc_buffer in case of no constraint folding with partition function.
```
  0de7ae1e
- Adds exe_path parameter to mirmap_runs.py and propagates it to each module. · d08c5df3
  cev authored Nov 09, 2012
  
  d08c5df3
- Makes eval_cons_bls and eval_selec_phylop compatible with N and lower case... · 29468862
  cev authored Nov 09, 2012
```
Makes eval_cons_bls and eval_selec_phylop compatible with N and lower case nucleotides in alignments.
```
  29468862
24 Oct, 2012 4 commits
- Adds dg_duplex_seed and dg_binding_seed features. · 8872059e
  cev authored Oct 24, 2012
  
  8872059e
- Small error in regex for RNAcofold. · 63a25d97
  cev authored Oct 24, 2012
  
  63a25d97
- Removes cevbio dependence in mirmap_runs.py. · 0e6d522f
  cev authored Oct 24, 2012
  
  0e6d522f
- Adds empty file empty.py. · 03b1c28f
  cev authored Oct 24, 2012
  
  03b1c28f
23 Oct, 2012 8 commits
- Adds phylofit() in if_exe_phast. · 064b6f1e
  cev authored Oct 23, 2012
  
  064b6f1e
- Removes prints. · 400b818e
  cev authored Oct 23, 2012
  
  400b818e
- Removes underscore in attributes (bug). · ba0f7527
  cev authored Oct 23, 2012
  
  ba0f7527
- Adds new interface (subprocess) for PHAST. · 2ee3606b
  cev authored Oct 23, 2012
  
  2ee3606b
- Moves comment. · 95d8dcbf
  cev authored Oct 23, 2012
  
  95d8dcbf
- Replaces tempdir that can be unset by gettempdir() in Spatt interface. · 8bde7be6
  cev authored Oct 23, 2012
  
  8bde7be6
- Replaces tempdir that can be unset by gettempdir(). Removes prints. · 6a9c3bed
  cev authored Oct 23, 2012
  
  6a9c3bed
- Adds new interface (subprocess) for Spatt. Adapts ctypes interface. · 2e24e563
  cev authored Oct 23, 2012
  
  2e24e563