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Created with Raphaël 2.2.015Jul141216Mar82128Feb22181210115Dec20Nov191312111030Oct292219719Aug181729Jun14May12111092Mar25Feb23181716108543228Jan262520151312614Nov24Oct23213128Sep22212018171612111095426Aug22211514131211829Jul181716107Jun6531May2120161413620Mar127Feb1925Jan121115Dec1074225Nov1918161512106543226Oct18171615985432128Sep25244231Aug21201916158615Jul141312109826Jun252422201918171615141312111095131May2322201916141310973130Apr29272520191612119654330Mar292827262319181714128528Feb272423211615131210Merge branch 'develop' into 'master'3.0.0 master3.0.0 masterCorrect r.scriptsdevelopdevelopAdd updated filters for BlUtBlUtBlUtMerge branch 'refactor' into 'develop'Update qusage fnctonrefactorrefactorReturn lin id to cluster and add by-cell id afterChange lin ID to single modeFix subsetHandle subsets if not all idents presentAdd mouse options and id lin by clusterFix labelsAdd back ribo filterChange ribo lower cutoff to 10% and change thresh scale to 0-255Revert nFeature lower cutoff to 200Change nFeature lower cutoff to 1000Fix stress/sampleAdd hard cutoff for nCount and a bunch of small stuffReplace left over hardwired mergeFix merge paramDouble [] for merge argRemove python load from bashFix opt argsAccept merge group from argsSignificant editsUpdate human references (to lung) and increase scAlign settingRemove tsne plotting from IDUp lin id res to 2Remove tsne from stress figsReduce n.neighbors for umap calc base on cell #Fix print umap onlyStop caclulating tsneAdd dynamic component calculation based on cell number (RAW)Remove IsoModes from threshFix up mouse ID (use res 1.0 for lin)Fix up mouse ID (use res 1.0 for lin)Add lower % ribo filterFix mergeSplit cutoff figs by sample namesMake sure sample names get set if loading from premade seurat objectsSpecify assay and slot for QUSAGE