{"push_id":569635800,"size":82,"distinct_size":6,"ref":"refs/heads/master","head":"27ded34c063d2b106faee2c769a065e96b1f8012","before":"218a511ae6048479d15471e7c5d78367be6384ef","commits":[{"sha":"9cb0985c67617e5d5f512f1511b5968a715fde9f","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"setting up OHSU sequencing data input/filtering:\nmoved stackedGeneBar to acc_functions.R\nadded argument indicating name of color matches file\nadded colorMatches file to extdata package folder","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/9cb0985c67617e5d5f512f1511b5968a715fde9f"},{"sha":"7c512f8a0b8c3116e8cd385acebb971bfd84b729","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"addition of cohort info to individual patients\nadded pathsummary to the path summary runner, made changes to summaryTable","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/7c512f8a0b8c3116e8cd385acebb971bfd84b729"},{"sha":"e16052f2bb80afcb03435f3f42944c0c3f07c4cc","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"improved output/readibility/understandability for settings list","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/e16052f2bb80afcb03435f3f42944c0c3f07c4cc"},{"sha":"e495034d6d638c52cc623fb9c6ef10b1459f54f0","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"add cohort info to individuals","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/e495034d6d638c52cc623fb9c6ef10b1459f54f0"},{"sha":"3ea0f4ab2018ba7f0536ec965cb9a8189cf96b07","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"Improved documentation of hypergeomentric path enrichment summaryTable plugin","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/3ea0f4ab2018ba7f0536ec965cb9a8189cf96b07"},{"sha":"3ae499ebd83dc383a82146ee904154dbe1613225","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"added arm for OHSU sequence capture data to the main program/fixed it up from the thesis version","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/3ae499ebd83dc383a82146ee904154dbe1613225"},{"sha":"e63db1dcd20c57dabcb8010a72511db064710cb7","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"fixed shiny drug select to allow negative filtering","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/e63db1dcd20c57dabcb8010a72511db064710cb7"},{"sha":"262ab0b01136484abad55a4219a03387a9a0009d","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"made this nicer to look at / use","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/262ab0b01136484abad55a4219a03387a9a0009d"},{"sha":"7a0d224fab706cc35034bbc7b177e4d8f1c5556b","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"manual integration tests passed","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/7a0d224fab706cc35034bbc7b177e4d8f1c5556b"},{"sha":"d502f86efa3b23ba53d2fb2977c1fe4550837c57","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"added examples to documentation","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/d502f86efa3b23ba53d2fb2977c1fe4550837c57"},{"sha":"2feacdc05e35d00600c6af9218b4fa4985b57221","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"modified top20hists function (shows dist of mutations across gene coordinates","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/2feacdc05e35d00600c6af9218b4fa4985b57221"},{"sha":"cdffbe975caa3c8bee2de9842a523806e8fe28aa","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"fixed combineAberrationTypes2, making the combination and ultimately overlap analysis work on individual patients when it the drug screen and aberration patients come from the same cohort","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/cdffbe975caa3c8bee2de9842a523806e8fe28aa"},{"sha":"b075888a4f3f1a3b2fc1e18c5fc389f9594ad9cc","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"fixed documentation/example to clear r cmd check","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/b075888a4f3f1a3b2fc1e18c5fc389f9594ad9cc"},{"sha":"1d96cef23824b7626893e95b0a67c65539a9a3bc","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"added diagnostic save to get path summary runner out","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/1d96cef23824b7626893e95b0a67c65539a9a3bc"},{"sha":"ea325f16c654b995568ee86cdab146793177ecdc","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"fixed up image saving and plot handling","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/ea325f16c654b995568ee86cdab146793177ecdc"},{"sha":"ab182eecbeeb3e2595051e2a06b58116171a91ff","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"fixed issue where combine aberration types was not adding aberration data when cohort was matched and had no coverage limitation","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/ab182eecbeeb3e2595051e2a06b58116171a91ff"},{"sha":"c0dd6492c9a1bb168eb97a33b98082577ac92704","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"fixed variable naming buggs and documentation","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/c0dd6492c9a1bb168eb97a33b98082577ac92704"},{"sha":"1988b58055bf8a09931d6dd9be4e7939995d6187","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"made image file save and move work correctly","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/1988b58055bf8a09931d6dd9be4e7939995d6187"},{"sha":"94ce908d108beed5ded521520023a842dffc686c","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"added line to add sequence capture arm","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/94ce908d108beed5ded521520023a842dffc686c"},{"sha":"b00f487dfbbbef052392bafbece844a46f047d20","author":{"email":"0199bdfc6ba3b9c10f3fafddfff16438237f79b9@hotmail.com","name":"samhiggins2001"},"message":"Fixed issue preventing input of single column of genes","distinct":false,"url":"https://api.github.com/repos/stochasticTreat/pathLayerDistributionVersion2/commits/b00f487dfbbbef052392bafbece844a46f047d20"}]}