commit-link" data-hovercard-type="commit" data-hovercard-url="https://github.com/raphael-group/machina/commit/d736439b9df1db6300018511006309157818a4c7/hovercard" href="https://github.com/raphael-group/machina/commit/d736439b9df1db6300018511006309157818a4c7">d736439 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Oct 5 18:45:26 2017 -0400 cleaned repo commit 7d6d6f0 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Oct 5 18:44:15 2017 -0400 cleaned repo commit 82e8a70 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Oct 5 17:38:16 2017 -0400 Cleaned up repo commit caf4dc1 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Oct 5 14:06:56 2017 -0400 Cleaning up repo commit 982fd70 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Oct 5 10:04:44 2017 -0400 Moved old ILPs into separate directory commit 71ba03f Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Wed Oct 4 13:28:08 2017 -0400 Cleaning up repo commit a945093 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Oct 4 13:05:33 2017 -0400 Cleaning up repository commit dfc771a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Oct 4 12:45:22 2017 -0400 Cleaning up repository commit cc0b550 Merge: 05514dc bb56e67 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Oct 1 16:09:01 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit 05514dc Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Oct 1 16:08:47 2017 -0400 Recall/precision of G commit bb56e67 Author: ragr2 <ragr2@nat-oitwireless-inside-vapornet100-c-18609.Princeton.EDU> Date: Fri Sep 29 16:16:09 2017 -0400 Hoadley treeomics analysis commit d566b65 Author: ragr2 <ragr2@nat-oitwireless-inside-vapornet100-c-18609.Princeton.EDU> Date: Fri Sep 29 15:27:46 2017 -0400 Hoadley treeomics figs commit abdf02e Author: ragr2 <ragr2@ragrs-MBP.fios-router.home> Date: Thu Sep 28 22:09:15 2017 -0400 Treeomics notebooks commit c38d040 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 28 15:44:32 2017 -0400 subclone detections commit cfd0b90 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 28 11:27:44 2017 -0400 Treeomics visualized trees commit 4f0e3c7 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 28 11:26:04 2017 -0400 Treeomics visualized trees commit 2d757fe Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 28 10:41:19 2017 -0400 Treeomics results commit ec957ed Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 28 10:29:53 2017 -0400 Treeomics commit 71fb54e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 28 08:52:13 2017 -0400 A7 treeomics commit e9d6edb Merge: 6c863a0 6058bb2 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Sep 27 18:45:23 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/finch into simulations commit 6c863a0 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Sep 27 18:43:47 2017 -0400 New A7 input file commit 6058bb2 Author: ragr2 <ragr2@ragrs-MBP.fios-router.home> Date: Wed Sep 27 11:10:31 2017 -0400 Updated bar plots commit 05cf9fc Author: ragr2 <ragr2@ragrs-MBP.fios-router.home> Date: Wed Sep 27 10:54:34 2017 -0400 Updated bar plots commit eb10c08 Merge: 0a641f7 86dfb64 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 26 19:24:30 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit 0a641f7 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 26 19:24:18 2017 -0400 Sanborn commit 86dfb64 Merge: f86cb5b a9bb37f Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 17:59:30 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/finch into simulations commit f86cb5b Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 17:59:25 2017 -0400 Plots updated commit a9bb37f Merge: 9d40c36 bbc175d Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 26 17:51:22 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit bbc175d Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 17:49:59 2017 -0400 Plots commit 9d40c36 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 26 17:46:13 2017 -0400 Makohon 2017, pancreatic commit bd4fca6 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 17:38:45 2017 -0400 plots commit 505811f Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 17:23:41 2017 -0400 plots commit 4251df2 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 17:19:17 2017 -0400 Plots updated commit c34878d Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 17:16:47 2017 -0400 New plots commit e731f50 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 16:56:15 2017 -0400 New plots commit 5b0f690 Author: ragr2 <ragr2@nat-oitwireless-inside-vapornet100-a-13624.Princeton.EDU> Date: Tue Sep 26 16:51:34 2017 -0400 Updated plotting scripts commit c513913 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 15:07:29 2017 -0400 Sim results commit 9ec7f9f Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 26 14:28:56 2017 -0400 Scripts commit 6d18baa Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 25 17:41:10 2017 -0400 Hot Start commit 98fbdf4 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 25 16:48:28 2017 -0400 Gundem et al. commit 1a706e7 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 24 20:41:24 2017 -0400 Results with only R pattern commit 426d1b9 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 24 17:46:17 2017 -0400 Tables commit e3a872b Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 24 16:16:00 2017 -0400 New tables commit b6dd6a4 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sat Sep 23 14:20:23 2017 -0400 MACHINA results commit 2fc18a7 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 22 22:20:08 2017 -0400 New MACHINA results commit 988eba8 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 22 21:42:43 2017 -0400 Scripts commit d358789 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 22 19:38:41 2017 -0400 Updated plots commit 5007846 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 22 09:39:20 2017 -0400 Simulation tables commit 9d0e7d5 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 17:43:34 2017 -0400 Sankoff commit 2070510 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 17:05:51 2017 -0400 MACHINA NO PR results commit 91c0e3d Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 16:52:39 2017 -0400 Treeomics results commit f1875e6 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 16:51:02 2017 -0400 MACHINA results commit 3ed92cb Merge: 8576bee b59ae83 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 16:37:45 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit 8576bee Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 16:37:25 2017 -0400 Treeomics results commit b59ae83 Author: Gryte Satas <gsatas7@gmail.com> Date: Thu Sep 21 16:17:00 2017 -0400 Updated results plots to exclude restritced results commit 4b5a354 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 15:28:41 2017 -0400 PMH_CTI commit aab79f5 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 21 15:25:54 2017 -0400 New option for PMH_CTI commit a657e0a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 21 11:23:23 2017 -0400 New MACHINA mut trees and clusters commit ad9e34e Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 11:06:41 2017 -0400 New simulations commit fb78d4a Merge: 6626221 96571f2 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 11:04:24 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit 6626221 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 11:03:07 2017 -0400 Cleanup commit 96571f2 Merge: 0f06ce7 19acb9d Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 11:01:26 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit 0f06ce7 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 21 11:01:14 2017 -0400 New simulations commit 19acb9d Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 21 10:06:15 2017 -0400 PMH_CTI no polytomy resolution option commit 00948b9 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 21 09:37:50 2017 -0400 Polyclonality check commit f9f4ab2 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 21 09:27:46 2017 -0400 Plots + Simulation Code update (correct polytomy handling and vertex labeling) commit 47bc8a7 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 21 09:07:47 2017 -0400 Plots + Simulation Code update (correct polytomy handling and vertex labeling) commit 3cc8e35 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 21 09:04:02 2017 -0400 Plots + Simulation Code update (correct polytomy handling and vertex labeling) commit 2a333cb Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 21 08:47:10 2017 -0400 Plots + Simulation Code update (correct polytomy handling and vertex labeling) commit 294f7ad Author: Gryte Satas <gsatas7@gmail.com> Date: Wed Sep 20 12:01:55 2017 -0400 Labeling count result files commit fd447c1 Author: Gryte Satas <gsatas7@gmail.com> Date: Tue Sep 19 22:55:23 2017 -0400 Labelling count plots commit 17c3fa0 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 19 14:15:29 2017 -0400 Updated font size commit 4cd9a9b Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 19 13:40:48 2017 -0400 Script to parse sankoff commit 9c5b904 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 19 13:25:56 2017 -0400 Made new ILPs the default option commit 19ec8f8 Merge: f9e8943 85e6603 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 19 11:05:44 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit f9e8943 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 19 11:05:34 2017 -0400 Updated Hoadley scripts commit 67ee21d Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 19 11:04:44 2017 -0400 Updated McPherson scripts commit 85e6603 Author: Gryte Satas <gsatas@ros.cs.princeton.edu> Date: Mon Sep 18 17:35:24 2017 -0400 Updated Table to include number of sites and inferred pattern commit 8e3983a Author: Gryte Satas <gsatas@ros.cs.princeton.edu> Date: Mon Sep 18 16:42:19 2017 -0400 Added scripts to make latex summary tables commit 0652109 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 18 12:03:34 2017 -0400 PMH commit 2fbf038 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 18 11:59:45 2017 -0400 PMH PR results commit aa4b9d2 Author: Gryte Satas <gsatas7@gmail.com> Date: Mon Sep 18 11:49:40 2017 -0400 Updated method order in plots commit 781c649 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 17 19:27:28 2017 -0400 New results commit ccd0bae Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 17 18:06:51 2017 -0400 New results commit 5f059b1 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 17 17:44:30 2017 -0400 MACHINA results commit d21d89e Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 17 08:15:05 2017 -0400 MACHINA results commit eefef5f Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 17 07:49:47 2017 -0400 Floating point issues and disabled IIS commit 9d68221 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 17 00:06:27 2017 -0400 Force root state to be equal to the root of the subtree as modeled by _zz commit e837626 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 16 00:36:59 2017 -0400 Outputting tree commit 3c6eac2 Merge: d00fd51 4e2ccaf Author: Gryte Satas <gsatas7@gmail.com> Date: Fri Sep 15 19:11:08 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulation commit d00fd51 Author: Gryte Satas <gsatas7@gmail.com> Date: Fri Sep 15 19:10:52 2017 -0400 Robinson-Foulds Violin Plots.ipynb commit 4e2ccaf Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 15 18:22:57 2017 -0400 Treeomics results commit 407e492 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 15 16:11:24 2017 -0400 New MACHINA clustered input commit 9314c23 Merge: 9d86c55 a50c61e Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 15 16:04:50 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit 9d86c55 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 15 16:04:39 2017 -0400 R m=8 instances commit b6f3769 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 15 15:43:06 2017 -0400 M m=8 instances commit e48fd14 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 15 15:25:04 2017 -0400 m=8 S instances commit a50c61e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 15 15:17:04 2017 -0400 Mutation not in mutation tree bug commit 30f1871 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 15 15:06:08 2017 -0400 m=8 mS instances commit 6a61216 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 15 14:49:54 2017 -0400 Fixed bug with M constraints commit 3867f4a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 15 14:23:49 2017 -0400 MACHINA input m=5 commit 5e03857 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 15 14:17:10 2017 -0400 Finished ILP PMH Solver commit c39100a Merge: d9c9ff1 d3708fb Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 15 00:54:06 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/finch into simulations commit d9c9ff1 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 15 00:54:01 2017 -0400 PMH CTI solver, fast and furious commit d3708fb Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 14 19:39:50 2017 -0400 R m=5 instances commit 06ec683 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 14 19:29:25 2017 -0400 M m=5 instances commit a8a76a0 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 14 19:19:11 2017 -0400 mS m=5 instances commit fb8d40e Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 14 19:10:47 2017 -0400 m5 S instances commit 111eb09 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 14 18:50:50 2017 -0400 Reverse BFS order commit 7cd7234 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 14 18:40:19 2017 -0400 New ILPs for PMH and PMH-PR. Updated cluster to output cell frequencies instead of VAFs commit d827151 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 12 20:17:03 2017 -0400 RF commit a812ff6 Merge: f41b09f e1bd43f Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 12 20:16:58 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/finch into simulations commit f41b09f Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 12 20:16:53 2017 -0400 RF commit e1bd43f Author: Gryte Satas <gsatas7@gmail.com> Date: Tue Sep 12 18:21:52 2017 -0400 Robinson-foulds plots commit dc5fc6b Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 12 12:58:43 2017 -0400 New NJ results commit 406878a Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 12 12:18:32 2017 -0400 New simulation m=8 commit 88c30ae Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 12 00:18:41 2017 -0400 Small number of mutation trees commit 902ffe9 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 12 00:18:14 2017 -0400 New instances commit 0cc498c Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 22:47:32 2017 -0400 Vertex labeling, exception with root vertex commit df2ac5c Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 22:34:29 2017 -0400 Multiple samples in primary commit cbb2a5a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 22:12:57 2017 -0400 Vertex labeling in simulations commit 62d06a7 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 21:48:27 2017 -0400 Vertex labeling in simulations commit 6f2fa50 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 20:20:04 2017 -0400 Migration graph determined more carefully commit e8b2ecc Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 20:14:59 2017 -0400 Migration graph determined more carefully commit 628dc45 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 20:09:45 2017 -0400 Migration graph determined more carefully commit 756db7c Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 19:38:21 2017 -0400 Migration graph determined more carefully commit 0fdda1b Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 18:53:53 2017 -0400 Migration graph determined more carefully commit ccc00a6 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 18:47:50 2017 -0400 Migration graph determined more carefully commit 91e5d24 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 18:45:23 2017 -0400 Migration graph determined more carefully commit af3e9f2 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 18:42:30 2017 -0400 Migration graph determined more carefully commit e2701c2 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 18:41:53 2017 -0400 Migration graph determined more carefully commit b572b1c Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 18:37:32 2017 -0400 Migration graph determined more carefully commit 638714a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 18:34:39 2017 -0400 Migration graph determined more carefully commit 81ec3a4 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 11 18:24:51 2017 -0400 Sims commit 22e0174 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 11 17:49:35 2017 -0400 Fixed migration graph commit 24cb29d Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 17:42:37 2017 -0400 Migration graph determined more carefully commit 9f05fa1 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 16:25:51 2017 -0400 #samples per anatomical site is a parameter commit 62369be Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 15:36:44 2017 -0400 Zero-ing out usages & freqs < 0.1 commit f017099 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 15:15:32 2017 -0400 Zero-ing out usages < 0.05 commit ee2b028 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 15:11:46 2017 -0400 Using binomial for variant reads, and zero-ing out freqs < 0.05 commit 69bb37e Merge: f5144f0 f015153 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 11 13:02:30 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit f5144f0 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 11 13:02:13 2017 -0400 MACHINA m5 results commit f015153 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 12:31:28 2017 -0400 Printing inferred clone tree instead of mutation tree in phm_cti output commit a48a521 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 11 11:58:46 2017 -0400 Relax leaf labeling to vertex labeling commit 60fe65b Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 20:21:50 2017 -0400 NJ results commit 1992939 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 10 19:43:31 2017 -0400 Treeomics results commit 7086c1d Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 10 19:20:07 2017 -0400 Clustering commit 59b3723 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 10 18:08:09 2017 -0400 New clustering based on new simulations commit 6dc975c Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 10 18:02:13 2017 -0400 New simulated instances commit 4cb094c Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 10 17:30:29 2017 -0400 Disable debug output commit 7fb3bc5 Merge: 378d121 10cf417 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 10 17:29:08 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit 378d121 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 10 17:28:58 2017 -0400 DEBUG output commit 10cf417 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 17:28:36 2017 -0400 Sampled mutations commit 6d718b7 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 16:25:26 2017 -0400 Simulations fixed bug in migration graph construction commit 9b96881 Merge: a801a07 85b2422 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 16:20:35 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/finch into simulations commit a801a07 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 16:20:31 2017 -0400 Simulations fixed bug in migration graph construction commit 85b2422 Author: Gryte Satas <gsatas7@gmail.com> Date: Sun Sep 10 16:07:48 2017 -0400 Objective value distribution plot commit c532e1b Merge: b4c023f 55de65c Author: Gryte Satas <gsatas7@gmail.com> Date: Sun Sep 10 15:16:40 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulation commit b4c023f Author: Gryte Satas <gsatas7@gmail.com> Date: Sun Sep 10 15:16:14 2017 -0400 Scripts for plotting robinson foulds distance commit 55de65c Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 14:50:24 2017 -0400 R was not detected commit 4810d90 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 14:17:03 2017 -0400 No bounds option for pmh_cti commit ccdf185 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 12:04:15 2017 -0400 Treeomics and neighbor joining results commit b02925a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 10:13:28 2017 -0400 Pick mutation trees commit a8e0147 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 01:18:52 2017 -0400 More output for pmh_cti commit e516de6 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 10 01:03:44 2017 -0400 Pmh_cti output commit 1241932 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sat Sep 9 17:09:35 2017 -0400 Clusters commit 9e2ec94 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 9 17:02:53 2017 -0400 Clustering commit 88f21ab Merge: e01d17b 793906d Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 9 16:20:29 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/finch into simulations commit e01d17b Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 9 16:20:24 2017 -0400 Making sure that Gabow-Myers respects time limit commit 793906d Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sat Sep 9 16:18:48 2017 -0400 Simulations contain only sampled mutations now commit fb8ef15 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 9 16:01:18 2017 -0400 Only mutations that are present in at least one sample are output in simulations. Various changes in pmh_cti commit 28719fe Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 9 13:34:32 2017 -0400 Clusters commit 5fe46d6 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 9 13:33:06 2017 -0400 Mutation tree enumeration commit b88f3ba Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 9 12:50:30 2017 -0400 Saving enumerated mutation trees in a single file commit 4e2ad11 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 8 15:46:16 2017 -0400 Fixed #samples commit c5e3f58 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 8 15:17:58 2017 -0400 Clustering based on connected components commit 69d94d7 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 8 12:19:39 2017 -0400 Renamed NonBinaryCloneTree to CloneTree commit 74593bc Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 8 11:56:18 2017 -0400 Removed binary clone tree commit 036e1fd Merge: 3755505 3e06827 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 8 11:28:23 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations commit 3755505 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 8 11:28:14 2017 -0400 Treeomics m=5 results commit 3e06827 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 8 11:09:25 2017 -0400 Outputting tree and labeling in msenumeration commit a92a69b Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 8 11:02:56 2017 -0400 Error-handling commit 8150e3f Merge: 7fb8765 81cbbe1 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 8 10:48:11 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/finch into simulations commit 7fb8765 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 8 10:48:01 2017 -0400 Error handling in visualizeclonetree commit 81cbbe1 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 7 23:43:07 2017 -0400 m5 treeomics input commit 84cdfaf Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 7 23:31:36 2017 -0400 New input instances commit c29e3dc Merge: 8c550e7 f98ef77 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 7 23:13:17 2017 -0400 Fixed conflict commit 8c550e7 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Sep 7 23:09:17 2017 -0400 Added m=5 instances commit f98ef77 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 7 22:48:17 2017 -0400 Changed objective of ILP commit 67d5f53 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 7 22:20:36 2017 -0400 Fixed mS enumeration commit 13fe496 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 7 15:31:22 2017 -0400 PMH_CTI works with multiple samples per anatomical sites now commit b3d6f7b Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 7 11:02:54 2017 -0400 Accepting input from stdin in generatemutationtrees commit 7cee98d Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 7 11:00:21 2017 -0400 Fixed bug in clustering commit b7cd924 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 7 10:58:15 2017 -0400 Fixed bug in clustering commit f6ccf0e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Sep 7 10:26:51 2017 -0400 Filter absent SNVs commit 99a3827 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Sep 6 19:04:24 2017 -0400 Clustering output commit 3f80b05 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Sep 6 18:55:04 2017 -0400 Limit on #canonical clone trees commit 8504d5e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Sep 6 18:52:30 2017 -0400 Limit on #mutation trees commit 5f02f44 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Sep 6 18:14:55 2017 -0400 Threading for enumeration commit 73e1e2d Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Wed Sep 6 18:05:43 2017 -0400 Generate mutation trees commit bb1fb4e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Sep 6 17:27:41 2017 -0400 enumeration commit 7a9266f Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Sep 6 17:03:14 2017 -0400 Clustering commit 7e5a487 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Wed Sep 6 13:51:31 2017 -0400 mS 200x coverage commit 7453783 Merge: b60dee6 c76de34 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 5 18:20:04 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/finch into simulations commit b60dee6 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 5 18:09:55 2017 -0400 Write read counts commit c76de34 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 5 17:15:30 2017 -0400 5000x mS commit 2692eb7 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 5 17:10:34 2017 -0400 New mS instances 5000x commit 668b49a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 5 17:08:29 2017 -0400 New parameter C commit 59fdd4d Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 5 17:06:57 2017 -0400 New parameter M commit 5877f4b Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 5 15:45:48 2017 -0400 mS 10 commit 6647724 Merge: ea65e60 6854ab5 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 5 15:43:44 2017 -0400 Merge branch 'simulations' of https://github.com/raphael-group/finch into simulations commit ea65e60 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 5 15:43:37 2017 -0400 Bootstrap commit 6854ab5 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 5 15:19:24 2017 -0400 Error-free mS commit ecee9a4 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 5 15:17:18 2017 -0400 Disable sequencing FP error commit 1906c2f Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 5 11:01:20 2017 -0400 Correct leaf labeling of simulated trees commit 3b84fe9 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Sep 5 10:54:55 2017 -0400 Updated tree labeling commit ada1ce8 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Tue Sep 5 10:33:03 2017 -0400 PyClone + TreeOmics commit a0f555c Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 4 22:25:10 2017 -0400 MAX parsimony commit 13df8e4 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 4 22:04:19 2017 -0400 PyClone commit 9b4a3ed Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 4 21:49:15 2017 -0400 Treeomics commit 97cbfb0 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 4 20:05:02 2017 -0400 Treeomics input commit 1da796d Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 4 15:52:23 2017 -0400 New simulations commit 6400544 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 4 15:31:04 2017 -0400 Relabeling anatomical sites commit 1545e9f Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 4 15:13:21 2017 -0400 Updated simulations commit a17250c Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 4 10:11:17 2017 -0400 Weighted migration rate commit bb0b5f7 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Mon Sep 4 08:46:54 2017 -0400 Selective pressure commit 2b0465c Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 4 00:35:35 2017 -0400 Roulette commit 2f9f8e0 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 4 00:31:36 2017 -0400 Roulette commit 59f188a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Sep 4 00:05:25 2017 -0400 Correct parameters commit e73ebdf Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 19:55:50 2017 -0400 Change of default parameters commit 8e7856d Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 19:50:52 2017 -0400 Dir times 5 commit 035a975 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 19:39:51 2017 -0400 Shared carrying capacity commit 93f1c62 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 19:18:34 2017 -0400 Drivers lead to more drivers commit bc76f31 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 19:09:24 2017 -0400 Starting from a driver commit 42a4672 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 18:59:30 2017 -0400 Migration commit cc95431 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 18:42:43 2017 -0400 Migration commit a395efc Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 18:27:21 2017 -0400 Migration commit e041dc6 Merge: 9489539 641db1a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 18:21:24 2017 -0400 Commit commit 9489539 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 18:20:23 2017 -0400 Removed extant cells commit 641db1a Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Sun Sep 3 18:18:41 2017 -0400 Carrying capacity depends on number of drivers commit 22fceaa Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Sep 3 17:03:18 2017 -0400 New simulations commit 22de7c5 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 2 12:18:16 2017 -0400 Maximum parsimony labeling commit 5f87597 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sat Sep 2 12:16:44 2017 -0400 NJ commit 8592f3d Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 1 21:00:38 2017 -0400 Simulations commit 3c442ef Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 1 20:42:54 2017 -0400 Generate script commit 58aebe6 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 1 20:41:27 2017 -0400 Resampled mixtures for R commit 28c83bf Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 1 20:33:38 2017 -0400 new R simulations commit 9320c3a Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Fri Sep 1 18:12:04 2017 -0400 Sequencing noise commit 5459b9a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 1 17:38:07 2017 -0400 Beta distribution commit 0f5a6ef Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 1 17:35:55 2017 -0400 Beta binomial commit 5f352e6 Author: Gryte Satas <gsatas7@gmail.com> Date: Fri Sep 1 15:16:50 2017 -0400 Simulation VAF plots commit 3358378 Author: Gryte Satas <gsatas7@gmail.com> Date: Fri Sep 1 15:11:10 2017 -0400 Simulation VAF plots commit 3b14589 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Sep 1 13:53:22 2017 -0400 Updated simulations commit 6f33346 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Aug 31 19:02:14 2017 -0400 R commit d21b18e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Aug 31 17:50:24 2017 -0400 Active anatomical sites commit bf26dd4 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Aug 31 16:50:09 2017 -0400 analysis notebook commit 0814e6e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Thu Aug 31 16:10:20 2017 -0400 Changed Dir threshold to 0.01 commit de23eb9 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Aug 31 11:24:41 2017 -0400 New S commit 5e2ceb0 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Aug 31 09:10:25 2017 -0400 mS commit a882469 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Aug 31 09:03:12 2017 -0400 New simulations commit 63a5525 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Thu Aug 31 09:00:04 2017 -0400 Changes to S, M and R migration commit 6482b95 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Aug 30 21:44:47 2017 -0400 Removed some asserts commit b8efd61 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Aug 30 21:34:24 2017 -0400 Observed G commit e33fa5c Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Aug 30 21:01:15 2017 -0400 Observations commit d69bb8e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Aug 30 19:25:11 2017 -0400 Observed clone tree commit 5654225 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Aug 30 10:47:05 2017 -0400 tumor -> tumour (PyClone) commit fe8e083 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Aug 30 10:38:59 2017 -0400 PyClone config files commit 4250b07 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Wed Aug 30 10:30:07 2017 -0400 PyClone simulation input commit 3ecbf66 Author: Mohammed El-Kebir <melkebir@cs.princeton.edu> Date: Wed Aug 30 09:09:04 2017 -0400 New simulations commit 9622b8e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 29 18:54:16 2017 -0400 Migration commit 776a7eb Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 29 18:38:19 2017 -0400 R and M (buffered migrations) commit e95c56d Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 29 18:28:10 2017 -0400 R and M commit e4c81a5 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 29 18:08:13 2017 -0400 Multi-graph commit 87bb300 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 29 18:05:31 2017 -0400 Patterns of migration commit 13c742c Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 29 16:33:09 2017 -0400 Read counts commit 234787e Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 29 14:02:34 2017 -0400 Maximum number of anatomical sites commit db44c9a Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 29 13:53:34 2017 -0400 Simulations commit 3064ccc Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 29 12:34:42 2017 -0400 Updated simulation code commit 5f52734 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Aug 28 16:43:47 2017 -0400 Simulations init commit commit 89881aa Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Fri Aug 25 18:02:34 2017 -0400 Gundem 2015 commit 6bb91f9 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 22 16:29:54 2017 -0400 Gundem et al. data commit 8785eab Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 22 16:16:48 2017 -0400 Gundem 2015 data commit 90865df Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 22 14:46:46 2017 -0400 Updated Hoadley scripts commit 4376d31 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 22 14:37:31 2017 -0400 Updated SPRUCE trees commit 7d3d295 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 22 14:33:38 2017 -0400 Cleaned up pmh_cti commit a9bf075 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Tue Aug 22 10:38:15 2017 -0400 Updated Gabow-Myers algorithm commit f1184c7 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Aug 21 19:56:43 2017 -0400 PR solver commit 74535a5 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Sun Aug 20 13:30:42 2017 -0400 SPRUCE for mS commit 3b3fee2 Author: Mohammed El-Kebir <melkebir@cs.brown.edu> Date: Mon Jul 3 13:10:08 2017 -0400 monclonal single-source seeding
-Original file line number
+Diff line change
 *.exe
 *.out
 *.app
 +.Rproj.user
++
 +doc/html/
 +build/
 +build2/
 +.ipynb_checkpoints/
++
 +# Mac stuff
 +.DS_store