{"push_id":567954541,"size":8,"distinct_size":2,"ref":"refs/heads/master","head":"1f0c6b2137d6edba1672ec25b3a76adff4a1619f","before":"64d6f59d0c41fee21f1219c9b104e823ff6f0e25","commits":[{"sha":"4ebf7526c75304554d49a55c0d23971832769bf3","author":{"email":"1b7fbefd792d7a9793d7aac527d8c759c32763c6@alumni.stanford.edu","name":"Frank Austin Nothaft"},"message":"[RNAdam-48] Added simple read simulator.","distinct":false,"url":"https://api.github.com/repos/niranjan93/RNAdam/commits/4ebf7526c75304554d49a55c0d23971832769bf3"},{"sha":"b2d0f6204a58095d10c4dc3394cf6589245a4f18","author":{"email":"9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","name":"Timothy Danford"},"message":"Merge pull request #49 from fnothaft/simple-sim\n\nAdds simple read simulator","distinct":false,"url":"https://api.github.com/repos/niranjan93/RNAdam/commits/b2d0f6204a58095d10c4dc3394cf6589245a4f18"},{"sha":"58a4d9a742e5bf86d3149fc8fe509899699ef939","author":{"email":"4dbe72d296c9f2cb7a93f2ebf0797ced7de34d9b@berkeley.edu","name":"Niranjan Kumar"},"message":"Changes were made to the m method in Quantify.scala so that the\n\"quantify unique transcripts\" sparkTest in QuantifySuite.scala\npasses. The problem was that in the m step of the EM algorithm,\nthe weight of equivalence class j for transcript i alpha_ji has\nto be multiplied by the fraction of k-mers in equivalence class j.\nThe Sailfish paper (Patro et al., 2014) does not include this\nin the EM algorithm equations it provides in the methods section.","distinct":false,"url":"https://api.github.com/repos/niranjan93/RNAdam/commits/58a4d9a742e5bf86d3149fc8fe509899699ef939"},{"sha":"e823b259dfb8b7f7d27aed1f9ab12e83d32af219","author":{"email":"9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","name":"Timothy Danford"},"message":"Merge pull request #51 from niranjan93/Quantify.apply_unit_tests\n\nModification to EM algorithm","distinct":false,"url":"https://api.github.com/repos/niranjan93/RNAdam/commits/e823b259dfb8b7f7d27aed1f9ab12e83d32af219"},{"sha":"c603429cba437858a5a648d728f0d280c04d1350","author":{"email":"1b7fbefd792d7a9793d7aac527d8c759c32763c6@alumni.stanford.edu","name":"Frank Austin Nothaft"},"message":"[RNAdam-50] Add more realistic transcript simulator.","distinct":false,"url":"https://api.github.com/repos/niranjan93/RNAdam/commits/c603429cba437858a5a648d728f0d280c04d1350"},{"sha":"16c5b2bf386eb45cb4cdd0d772942c2d5af2d08e","author":{"email":"9dcf5e33cfb31a2872893d1fd44fa7914cac0864@users.noreply.github.com","name":"Timothy Danford"},"message":"Merge pull request #52 from fnothaft/transcript-generator\n\n[RNAdam-50] Add more realistic transcript simulator.","distinct":false,"url":"https://api.github.com/repos/niranjan93/RNAdam/commits/16c5b2bf386eb45cb4cdd0d772942c2d5af2d08e"},{"sha":"ba8561e2d05a862d622c7d6988535019f4a1ef34","author":{"email":"1b7fbefd792d7a9793d7aac527d8c759c32763c6@alumni.stanford.edu","name":"Frank Austin Nothaft"},"message":"[RNAdam-54] Add linear regression stage for calibrating k-mer counts vs. sequence context percentage.","distinct":true,"url":"https://api.github.com/repos/niranjan93/RNAdam/commits/ba8561e2d05a862d622c7d6988535019f4a1ef34"},{"sha":"1f0c6b2137d6edba1672ec25b3a76adff4a1619f","author":{"email":"9dcf5e33cfb31a2872893d1fd44fa7914cac0864@users.noreply.github.com","name":"Timothy Danford"},"message":"Merge pull request #56 from fnothaft/calibrate-kmers\n\nAdd regression based technique for calibrating k-mer counts","distinct":true,"url":"https://api.github.com/repos/niranjan93/RNAdam/commits/1f0c6b2137d6edba1672ec25b3a76adff4a1619f"}]}