| f8df857 | shermin | 04 January 2017, 19:23:06 UTC | Commit prior to submitting paper. Should be working. Need to add function to take in fasta/fastq data and calculate NCM enrichment. | 04 January 2017, 19:23:06 UTC |
| b65c3e6 | shermin | 21 September 2016, 18:06:49 UTC | generalize mysql calls to include table names as arguments. updates to standardize ncm calc in cal-structure-features | 21 September 2016, 18:06:49 UTC |
| ceecab3 | shermin | 07 July 2016, 03:00:38 UTC | updated readme for some usage information | 07 July 2016, 03:00:38 UTC |
| a985cd8 | shermin | 30 June 2016, 18:31:19 UTC | pre-publication commit | 30 June 2016, 18:31:19 UTC |
| 5083a44 | shermin | 12 May 2016, 17:57:43 UTC | rewrote potential stacks and get motifs so that they would also track the helix/stem lengths. This is in preparation to change the way stack motifs are defined and make more modular the stack motif definition parameters | 12 May 2016, 17:57:43 UTC |
| 8a94b30 | shermin | 06 May 2016, 14:23:30 UTC | last working copy for motifs-by-round9. changed to count relative position and helix length in motifs-by-round10 | 06 May 2016, 14:23:30 UTC |
| c08bd0b | shermin | 29 October 2015, 19:56:31 UTC | refactoring the way the fastq to table method is done to break up the monolithic function that was. Now functions produce nulls for mysql when there is no data. Some globals were added as well so that we know where the files are and which rounds they correspond to. | 29 October 2015, 19:56:31 UTC |
| c523872 | shermin | 25 August 2015, 17:19:11 UTC | added reversev to utils.clj. updated the make-pair-table name for refold. changes to analysis just to keep up to date on current analysis methods. Updated project file to reflect server vs self testing profiles. fold-ops now use conch instead of clojure.java.shell | 25 August 2015, 17:19:11 UTC |
| 604bab2 | shermin | 21 July 2015, 15:52:30 UTC | returns deltaG as part of folding output. Also added a function to calculate centroid structures for sequences in a fasta file | 21 July 2015, 15:52:30 UTC |
| de3f3bd | shermin | 07 March 2015, 20:09:46 UTC | added clj from tangling results | 07 March 2015, 20:09:46 UTC |
| 69b4a9b | shermin | 09 December 2014, 18:48:40 UTC | added analysis files which are generated from literate programming files using org+babel. Updates were done to utils and summary stats. get-seqs in utils will be modified again to include more options. | 09 December 2014, 18:48:40 UTC |
| 1a51b14 | shermin | 21 November 2014, 15:23:30 UTC | update to the new clojure1.6. also major comit changes changing the way data is accessed in mysql as opposed to fasta | 21 November 2014, 15:23:30 UTC |
| bc204fd | Meyerlab | 30 July 2014, 23:19:40 UTC | update functions for EM in hmm. added additional query to test sql cases | 30 July 2014, 23:19:40 UTC |
| 6d115e0 | Meyerlab | 26 July 2014, 02:19:22 UTC | updates to queries and baum welch algorithm | 26 July 2014, 02:19:22 UTC |
| 645b95b | Meyerlab | 23 July 2014, 22:06:15 UTC | tree traversal with branch length | 23 July 2014, 22:06:15 UTC |
| 1779374 | shermin pei | 22 July 2014, 03:26:18 UTC | added code for hmm | 22 July 2014, 03:26:18 UTC |
| 1ed9ede | Meyerlab | 16 July 2014, 22:45:07 UTC | figured out how to traverse the tree and add weights | 16 July 2014, 22:45:07 UTC |
| de90ba1 | shermin | 16 July 2014, 15:31:05 UTC | added upgma and more functions to utils. Also there are some core mysql queries added. | 16 July 2014, 15:31:05 UTC |
| 8ffda15 | shermin | 25 June 2014, 00:15:26 UTC | daily commit | 25 June 2014, 00:15:26 UTC |
| faee29e | shermin | 20 June 2014, 18:08:15 UTC | initial commit | 20 June 2014, 18:08:15 UTC |
