| 2416572 | Jason Piper | 30 May 2016, 01:18:22 UTC | Update contact details and bump to 0.2.4 | 30 May 2016, 01:18:22 UTC |
| 84ff434 | Jason Piper | 17 January 2016, 09:21:27 UTC | Fix empty ∆FP output | 17 January 2016, 09:21:27 UTC |
| 00167d7 | Jason Piper | 25 November 2015, 22:42:40 UTC | Fix wellington_bootstrap.py error, push to v0.2.2 | 25 November 2015, 22:42:40 UTC |
| b3def9f | Jason Piper | 25 November 2015, 15:28:15 UTC | Enable ATAC-seq mode, bump to v0.2.1 | 25 November 2015, 15:28:15 UTC |
| 5029f59 | Jason Piper | 25 November 2015, 13:47:54 UTC | Update README with latest journal article | 25 November 2015, 13:47:54 UTC |
| d7da79b | Jason Piper | 19 November 2015, 01:33:17 UTC | Update build badges to SVG | 19 November 2015, 01:33:17 UTC |
| 3a09318 | Jason Piper | 18 November 2015, 10:01:47 UTC | bump to version 0.2.0 | 18 November 2015, 10:01:47 UTC |
| a4c2a2e | Jason Piper | 18 November 2015, 10:00:41 UTC | Merge branch 'ATAC' | 18 November 2015, 10:00:41 UTC |
| 097ce2e | Jason Piper | 18 November 2015, 09:57:14 UTC | Updated documentation | 18 November 2015, 09:57:14 UTC |
| 8231a02 | Jason Piper | 08 June 2015, 09:54:28 UTC | More ATAC compatibility | 08 June 2015, 09:54:28 UTC |
| e5bd52d | Jason Piper | 07 June 2015, 15:44:21 UTC | Add progress bar to FOS script | 07 June 2015, 15:44:21 UTC |
| dc0eb01 | Jason Piper | 07 June 2015, 14:35:40 UTC | Update documentation references to ATAC | 07 June 2015, 14:35:40 UTC |
| f64991d | Jason Piper | 07 June 2015, 14:35:22 UTC | Wellington1D Fix and Cythonize | 07 June 2015, 14:35:22 UTC |
| 65e6515 | Jason Piper | 07 June 2015, 06:52:35 UTC | Fix footprinting script typo | 07 June 2015, 06:52:35 UTC |
| 65aaa5b | Jason Piper | 07 June 2015, 02:25:48 UTC | ATAC-seq support | 07 June 2015, 02:25:48 UTC |
| 65ee38b | Jason Piper | 09 May 2015, 04:49:36 UTC | Amend requirements | 09 May 2015, 04:49:36 UTC |
| 1fd88a8 | Jason Piper | 08 May 2015, 09:45:14 UTC | Cleanup differential footprinting script Model model parameterisation via command line arguments, more PEP8 compliance, removal of crud code | 08 May 2015, 09:45:14 UTC |
| c5b62f2 | Jason Piper | 08 May 2015, 05:44:02 UTC | Add wellington bootstrap to pip distribution | 08 May 2015, 05:44:02 UTC |
| 5c3380f | Jason Piper | 16 April 2015, 10:24:47 UTC | Cython no longer required (although some dependencies may require them…) | 16 April 2015, 10:24:47 UTC |
| 3751f30 | Jason Piper | 16 April 2015, 10:17:15 UTC | Why. Won't. You. Build. | 16 April 2015, 10:17:15 UTC |
| f47d6aa | Jason Piper | 16 April 2015, 10:02:01 UTC | Check chromosome sizes This ensures that we don’t elongate beyond the end of the chromosome | 16 April 2015, 10:02:01 UTC |
| 11a0b69 | Jason Piper | 16 April 2015, 09:57:51 UTC | Fix installation issues | 16 April 2015, 09:57:51 UTC |
| 8d8ee7e | Jason Piper | 15 April 2015, 18:06:58 UTC | Fix build | 15 April 2015, 18:06:58 UTC |
| bcf6027 | Jason Piper | 15 April 2015, 15:50:57 UTC | Added script to estimate 6-mer cleavage bias | 15 April 2015, 15:50:57 UTC |
| e6fee79 | Jason Piper | 12 April 2015, 22:20:27 UTC | Initial Differential Footprinting Script. Desperately needs refactoring | 12 April 2015, 22:20:27 UTC |
| 03d5d89 | Jason Piper | 08 December 2014, 18:34:35 UTC | Fix regression caused by numpy array removal | 08 December 2014, 18:34:35 UTC |
| f92d941 | Jason Piper | 14 November 2014, 11:49:33 UTC | Error checking for bias plotting | 14 November 2014, 11:49:33 UTC |
| 9e09c6f | Jason Piper | 14 November 2014, 11:49:09 UTC | Add preliminary tutorial to documentation | 14 November 2014, 11:49:09 UTC |
| c5ac70a | Jason Piper | 14 November 2014, 11:44:21 UTC | Add ∆DHS scoring script | 14 November 2014, 11:44:21 UTC |
| aff589d | Jason Piper | 18 September 2014, 07:37:27 UTC | remove erroneous debug message | 18 September 2014, 07:37:27 UTC |
| b1c1025 | Jason Piper | 03 September 2014, 18:13:37 UTC | Fix caching bug | 03 September 2014, 18:13:37 UTC |
| 8623d0c | Jason Piper | 03 September 2014, 18:12:47 UTC | 0.1.7 - Fix caching issue | 03 September 2014, 18:12:47 UTC |
| ca78df5 | Jason Piper | 02 September 2014, 19:12:23 UTC | fix formatting | 02 September 2014, 19:12:23 UTC |
| 9564f41 | Jason Piper | 02 September 2014, 19:11:30 UTC | script to annotate bed file with DNase cuts | 02 September 2014, 19:11:30 UTC |
| 65653f3 | Jason Piper | 02 September 2014, 19:06:17 UTC | Another FAQ | 02 September 2014, 19:06:17 UTC |
| b5bbb7e | Jason Piper | 02 September 2014, 19:05:58 UTC | Ability to purge BAMHandler cache | 02 September 2014, 19:05:58 UTC |
| e0487e9 | Jason Piper | 01 September 2014, 20:38:17 UTC | Fix script install | 01 September 2014, 20:38:17 UTC |
| 10198fe | Jason Piper | 28 July 2014, 21:43:19 UTC | Remove old code Hopefully this fixes the build as well | 28 July 2014, 21:43:19 UTC |
| 59fbb31 | Jason Piper | 28 July 2014, 20:27:24 UTC | Some documentation for bias correction | 28 July 2014, 20:27:24 UTC |
| 54f0cab | Jason Piper | 28 July 2014, 20:26:52 UTC | Remove references to numpy in docs | 28 July 2014, 20:26:52 UTC |
| 5f6521e | Jason Piper | 28 July 2014, 18:55:17 UTC | fix example command line parameters | 28 July 2014, 18:55:17 UTC |
| 465c0f0 | Jason Piper | 28 July 2014, 18:53:50 UTC | Preliminary bias correction | 28 July 2014, 18:53:50 UTC |
| 5d5ae8d | Jason Piper | 26 July 2014, 11:11:09 UTC | Disable wobble and growth/shrink | 26 July 2014, 11:11:09 UTC |
| 50b3891 | Jason Piper | 24 June 2014, 18:53:38 UTC | Merge pull request #9 from ajank/master Fixing a syntax error in bedtools invocation | 24 June 2014, 18:53:38 UTC |
| 2934d99 | Aleksander Jankowski | 24 June 2014, 18:31:02 UTC | Fixing a syntax error in bedtools invocation | 24 June 2014, 18:31:02 UTC |
| 288650c | Jason Piper | 27 May 2014, 21:18:51 UTC | Update with the new score. | 27 May 2014, 21:18:51 UTC |
| 2fefd88 | Jason Piper | 23 May 2014, 23:44:45 UTC | Markus' new ∆FP-ing algorithm | 23 May 2014, 23:44:45 UTC |
| c407d0e | Jason Piper | 12 April 2014, 16:34:29 UTC | sexy document theme | 12 April 2014, 16:34:29 UTC |
| 77cb1ad | Jason Piper | 12 April 2014, 16:28:15 UTC | Sexy documentation | 12 April 2014, 16:28:15 UTC |
| 30160ad | Jason Piper | 12 April 2014, 16:11:36 UTC | NumPy not needed pre-install anymore | 12 April 2014, 16:11:36 UTC |
| 66bb01f | Jason Piper | 12 April 2014, 15:52:54 UTC | New Cython compiled code | 12 April 2014, 15:52:54 UTC |
| 4fa0978 | Jason Piper | 12 April 2014, 15:51:27 UTC | Another Cython type change I think I’m just getting pedantic now | 12 April 2014, 15:51:27 UTC |
| 4b1bba5 | Jason Piper | 12 April 2014, 15:50:54 UTC | Implementation of Markus' differential footprints This doesn’t appear to work, but it may be that I’ve implemented this incorrectly. | 12 April 2014, 15:50:54 UTC |
| 270ed18 | Jason Piper | 12 April 2014, 15:14:45 UTC | Cleaned up some Cython types | 12 April 2014, 15:14:45 UTC |
| 4e65e23 | Jason Piper | 12 April 2014, 15:14:07 UTC | Fix FOS to account for footprint size | 12 April 2014, 15:14:07 UTC |
| fccade1 | Jason Piper | 11 April 2014, 17:12:19 UTC | Change the sentinel value to -1 | 11 April 2014, 17:12:19 UTC |
| dcde0a6 | Jason Piper | 11 April 2014, 16:01:45 UTC | Update the method footprints are called We had comments that footprints were fairly large by default. This was caused by the way in which we called footprints from the footprint p-values. This is a putative fix that changes the way footprints are called to try and sort this out. | 11 April 2014, 16:01:45 UTC |
| 7eec3b1 | Jason Piper | 10 April 2014, 09:59:08 UTC | Add test for BAM handler without caching | 10 April 2014, 09:59:08 UTC |
| 9f336ac | Jason Piper | 10 April 2014, 08:09:04 UTC | Added a few convenience scripts | 10 April 2014, 08:09:04 UTC |
| 8b38d1d | Jason Piper | 07 April 2014, 16:57:33 UTC | fix FOS | 07 April 2014, 16:57:33 UTC |
| 7521ee4 | Jason Piper | 07 April 2014, 15:30:16 UTC | Let's disable shoulder shrinkage for the moment. | 07 April 2014, 15:30:16 UTC |
| eea4d92 | Jason Piper | 07 April 2014, 15:28:47 UTC | Add output randomisation | 07 April 2014, 15:28:47 UTC |
| 771de14 | Jason Piper | 07 April 2014, 15:27:57 UTC | Change asserting to exception | 07 April 2014, 15:27:57 UTC |
| 05ca501 | Jason Piper | 07 April 2014, 15:27:42 UTC | Fix FDR shuffling | 07 April 2014, 15:27:42 UTC |
| 293a4e8 | Jason Piper | 07 March 2014, 11:17:36 UTC | 0.1.6 - Actually perform FDR iterations Massive thanks to @arjanvandervelde for spotting this! | 07 March 2014, 11:17:36 UTC |
| fd20d81 | Jason Piper | 07 March 2014, 11:10:04 UTC | Actually perform FDR Calculation Massive thanks to @arjanvandervelde! | 07 March 2014, 11:10:04 UTC |
| d35339f | Jason Piper | 20 February 2014, 14:24:21 UTC | Fixes in Differential Footprinting | 20 February 2014, 14:24:21 UTC |
| 17e867c | Jason Piper | 20 February 2014, 14:23:54 UTC | Allow for normalisation of cutting bias | 20 February 2014, 14:23:54 UTC |
| 9576548 | Jason Piper | 20 February 2014, 14:23:26 UTC | Fix rounding to -inf | 20 February 2014, 14:23:26 UTC |
| 22067ca | Jason Piper | 20 February 2014, 14:22:56 UTC | Fix cut bias estimation | 20 February 2014, 14:22:56 UTC |
| 6d943de | Jason Piper | 17 February 2014, 10:22:43 UTC | Sanity check on interval size for footprinting | 17 February 2014, 10:22:43 UTC |
| 5f1a28b | Jason Piper | 15 February 2014, 16:01:55 UTC | Fix memory leaks, bring algorithm in line with previous Python implementation | 15 February 2014, 16:01:55 UTC |
| 3db4b5b | Jason Piper | 15 February 2014, 15:28:30 UTC | First attempt at differential Footprinting in C | 15 February 2014, 15:28:30 UTC |
| 79c6a0b | Jason Piper | 14 February 2014, 14:38:11 UTC | Update unit test for footprinting lengths | 14 February 2014, 14:38:11 UTC |
| 5214d0d | Jason Piper | 14 February 2014, 14:35:06 UTC | Clean up C implementation | 14 February 2014, 14:35:06 UTC |
| 712e894 | Jason Piper | 14 February 2014, 12:56:56 UTC | Explicitly enable C99 | 14 February 2014, 12:56:56 UTC |
| 1bff4b4 | Jason Piper | 14 February 2014, 12:39:23 UTC | Replace Wellington with pure C implementation This yields a roughly 4x speed increase - not too amazing but nothing to turn your nose up at | 14 February 2014, 12:39:23 UTC |
| f25b4d9 | Jason Piper | 12 February 2014, 19:24:10 UTC | Enable cut normalisation as fraction of total cuts in region | 12 February 2014, 19:24:10 UTC |
| b5715d6 | Jason Piper | 12 February 2014, 16:36:59 UTC | Add ability to merge strands, update colour scheme The Red/Blue colour scheme is much more prominent in the literature at the moment. | 12 February 2014, 16:36:59 UTC |
| 6588f01 | Jason Piper | 03 February 2014, 10:08:50 UTC | Fix for np.array deprecation | 03 February 2014, 10:08:50 UTC |
| 4e5785b | Jason Piper | 31 January 2014, 12:34:01 UTC | 0.1.5 | 31 January 2014, 12:34:01 UTC |
| 9bc1db7 | Jason Piper | 31 January 2014, 12:33:57 UTC | Fixed wig file format for UCSC | 31 January 2014, 12:33:57 UTC |
| 8334df3 | Jason Piper | 29 January 2014, 16:33:12 UTC | Badges! | 29 January 2014, 16:33:31 UTC |
| a704b06 | Jason Piper | 29 January 2014, 16:33:12 UTC | Badges! | 29 January 2014, 16:33:12 UTC |
| eb90937 | Jason Piper | 29 January 2014, 16:09:11 UTC | Add coveralls support | 29 January 2014, 16:10:41 UTC |
| a13ded1 | Jason Piper | 29 January 2014, 16:09:11 UTC | Add coveralls support | 29 January 2014, 16:09:11 UTC |
| ad2e3bd | Jason Piper | 29 January 2014, 14:24:24 UTC | Finish removing SciPy dependency | 29 January 2014, 14:24:24 UTC |
| 03857c9 | Jason Piper | 29 January 2014, 12:08:35 UTC | Travis: Fix builds | 29 January 2014, 14:03:00 UTC |
| 36a1ca8 | Jason Piper | 29 January 2014, 13:49:22 UTC | Remove SciPy dependency | 29 January 2014, 14:02:21 UTC |
| 48e8317 | Jason Piper | 29 January 2014, 09:53:07 UTC | First pass at travis-ci | 29 January 2014, 14:01:22 UTC |
| 6f90fae | Jason Piper | 29 January 2014, 13:49:22 UTC | Remove SciPy dependency | 29 January 2014, 13:49:24 UTC |
| fca705e | Jason Piper | 29 January 2014, 13:27:48 UTC | Test removing scipy dependency | 29 January 2014, 13:27:48 UTC |
| adef797 | Jason Piper | 29 January 2014, 12:08:35 UTC | Travis: Fix builds | 29 January 2014, 12:08:35 UTC |
| 73ff5ca | Jason Piper | 29 January 2014, 10:18:56 UTC | Fix dependencies for new installations | 29 January 2014, 10:24:37 UTC |
| 1571f07 | Jason Piper | 29 January 2014, 10:18:56 UTC | Fix versioning | 29 January 2014, 10:18:56 UTC |
| b772aac | Jason Piper | 29 January 2014, 09:53:07 UTC | First pass at travis-ci | 29 January 2014, 09:53:07 UTC |
| 1a1f1c8 | Jason Piper | 24 January 2014, 11:50:41 UTC | Update README with numpy to list API change | 24 January 2014, 11:50:41 UTC |
| 3813711 | Jason Piper | 24 January 2014, 11:07:40 UTC | Whoops | 24 January 2014, 11:07:40 UTC |
| 1abf71c | Jason Piper | 24 January 2014, 11:04:27 UTC | Merge upstream changes from MASTER | 24 January 2014, 11:04:27 UTC |
| a63a4d1 | Jason Piper | 24 January 2014, 10:42:10 UTC | No need for **kwargs here | 24 January 2014, 10:42:10 UTC |
