{"push_id":847738244,"size":7,"distinct_size":7,"ref":"refs/heads/master","head":"0e8ecb769a92ab18eafb82b1348ce95daa6032bf","before":"01e821ae857c3d11dc134e42bc3c7c448f20c493","commits":[{"sha":"02f084223dafb35a7e5baa101a490287f51f4d81","author":{"email":"5d4d3e06f787f19ee8bd2c22bf6a3665f33c44aa@gmail.com","name":"Tim Triche, Jr"},"message":"Merge pull request #16 from ttriche/master\n\nMerging -- this is stable (or at least, stable enough that I now use it several times a day, every day.)","distinct":true,"url":"https://api.github.com/repos/ttriche/artemis/commits/02f084223dafb35a7e5baa101a490287f51f4d81"},{"sha":"896c5a57cd7f57ae59481edd1afa0129a183f9d4","author":{"email":"6768d5a95fe7d2186d456a9939f033d68f22aee2@gmail.com","name":"Anthony R. Colombo"},"message":"updating the annotation to include RepDb\n\nThis is tested on my branch. works.","distinct":true,"url":"https://api.github.com/repos/ttriche/artemis/commits/896c5a57cd7f57ae59481edd1afa0129a183f9d4"},{"sha":"a431d9d98afd3a2119f1c717c5d3d01fec13797b","author":{"email":"6768d5a95fe7d2186d456a9939f033d68f22aee2@gmail.com","name":"Anthony R. Colombo"},"message":"species argument and switch argument species\n\nThe previous match.arg(species) was a type because it was missing the second argument to match from the catalog.  so this fix requires a user to enter geneWiseAnalysis(kexp, ... species=\"Homo.sapiens\")  ; user must specify species of interest.\r\n\r\nthis line  species <- match.arg(species, c(\"Homo.sapiens\",\r\n                                       \"Mus.musculus\",\r\n                                       \"Rattus.norvegicus\"))\r\n\r\nwill then yank out the species.  *The technically correct way of doing this is with a hash table*","distinct":true,"url":"https://api.github.com/repos/ttriche/artemis/commits/a431d9d98afd3a2119f1c717c5d3d01fec13797b"},{"sha":"454e5a4fad83e97366af01ef9095323be5ddfce6","author":{"email":"6768d5a95fe7d2186d456a9939f033d68f22aee2@gmail.com","name":"Anthony R. Colombo"},"message":"Output limma expression values, with Meta info\n\nHere is a summary that was tested on arcolombo/artemis  RAM branch.  this worked for the beta- version testing.  The motivation was due to Kwasi's request of having the differential expression with the meta-information.  this required data handling between features of genomic ranges, and limma outputs.\r\n\r\n\r\nthe issue is stemming from an early development decision to keep outputs in terms of ensembl gene IDs.  In order to use Reactome, this requires a mapping via biomaRt in terms of entrez id.    \r\n\r\nSummary:\r\nlines  81-101  perform   ensemblGene_ID -> entrez id  dependent on commonName derived from match.arg input from user.  this is standard and performed successfully from arcolombo/artemis ~ RAM. \r\n    -reactome is performed on the object converted[,2] which is all the non - na  entrez Ids.\r\n\r\nline 120  runs a scaled transformation of limma values, but these values are in terms of ensembl ID,  so ensemblVector, are all the corresponding entries with non-na  entrez ID.  \r\n\r\n\r\nlines 128-132  is over-coding in an attempt to protect the use of the \"which\" command.  here is the logic:\r\n                      the ensemblVector is the first column of a data frame which stores all the non-NA entrez ID mapped by biomaRt.  \r\n                      each column ensemblVector and entrezVector has identical rows.  \r\n                      limma is performed on ensemblVector created res$scaledExprs and outputs ensembl IDs\r\n                      line 123 converts the limma outputs to entrez with non-NA.\r\n                      line 146 creates G_list that has human gene nomenclature\r\n                      lines 156-181  create a merge between limma expression and meta information from features(kexp).\r\n\r\nLines 156-181 could be omitted if deemed unnecessary.  However lines 81-141 perform reactome and necessary ensembl -> entrez mapping.","distinct":true,"url":"https://api.github.com/repos/ttriche/artemis/commits/454e5a4fad83e97366af01ef9095323be5ddfce6"},{"sha":"6ebc769a185ec43b349b11c52b881ac8573dc7d1","author":{"email":"5d4d3e06f787f19ee8bd2c22bf6a3665f33c44aa@gmail.com","name":"Tim Triche, Jr"},"message":"Merge pull request #18 from RamsinghLab/arcolombo-patch-1\n\nspecies argument and switch argument species\r\nauto merging","distinct":true,"url":"https://api.github.com/repos/ttriche/artemis/commits/6ebc769a185ec43b349b11c52b881ac8573dc7d1"},{"sha":"a22eb5305bbce0d16d43607f042de1f92fffce26","author":{"email":"5d4d3e06f787f19ee8bd2c22bf6a3665f33c44aa@gmail.com","name":"Tim Triche, Jr"},"message":"Merge pull request #19 from RamsinghLab/arcolombo-patch-genewiseanalysis\n\nOutput limma expression values, with Meta info\r\n\r\nauto merging","distinct":true,"url":"https://api.github.com/repos/ttriche/artemis/commits/a22eb5305bbce0d16d43607f042de1f92fffce26"},{"sha":"0e8ecb769a92ab18eafb82b1348ce95daa6032bf","author":{"email":"5d4d3e06f787f19ee8bd2c22bf6a3665f33c44aa@gmail.com","name":"ttriche"},"message":"Merge remote-tracking branch 'upstream/master'\n\nConflicts:\n\tR/annotateBundles.R\n\tR/geneWiseAnalysis.R","distinct":true,"url":"https://api.github.com/repos/ttriche/artemis/commits/0e8ecb769a92ab18eafb82b1348ce95daa6032bf"}]}