Search.setIndex({docnames:["api/index","basic_usage","examples","index","installation","references","release_notes"],envversion:53,filenames:["api/index.rst","basic_usage.rst","examples.rst","index.rst","installation.rst","references.rst","release_notes.rst"],objects:{episcanpy:{api:[0,0,0,"-"]}},objnames:{"0":["py","module","Python module"]},objtypes:{"0":"py:module"},terms:{"10x":2,"68k":2,"class":1,"default":1,"float":1,"function":1,"import":[0,1],"return":1,"true":1,"var":1,Axes:1,For:[0,1,2],The:[1,2,3],Then:4,access:[1,4],adata:1,adata_subset:1,add:1,all:1,allow:1,also:[1,3,6],altern:1,amir13:5,amir:5,analys:[2,3],analysi:1,anim:2,anndata:[3,6],anno:1,annot:1,api:1,append:1,associ:1,atacseq:3,avail:3,axes:1,base:1,basic:1,batch:0,behind:2,biologi:3,biotechnolog:5,blablabla:[3,6],blog:1,bsseq:3,call:1,can:[1,2],categor:1,cell:[0,1,5],cell_group:1,chromatin:3,cite:[2,3],cluster:2,code:3,come:3,compar:2,compat:3,complex:2,conda:4,configur:1,consid:[3,4],consist:1,contain:2,control:0,copi:1,correct:0,could:1,creat:4,current:2,data:[1,3,5],datafram:1,dataset:2,describ:2,detail:1,dict:1,diffus:2,dimension:5,document:3,doi:2,done:2,each:1,easili:1,effect:0,effici:1,emb:1,enabl:5,epi:[0,1],episcanpi:[0,1,4],exampl:[1,2],express:1,extend:2,extract_cg:0,extract_ch:0,facilit:1,fals:1,file:1,filenam:1,filename_sample_annot:1,filter:0,follow:2,forg:4,from:[2,3,4],further:1,gene:[0,1,2],genom:[2,3],get:2,github:3,haghverdi16:2,have:[1,4],hematopoiesi:2,here:2,heterogen:5,high:[0,5],highli:0,http:3,identif:2,igraph:4,implement:3,index:[],infer:2,initi:1,inplac:1,instal:3,instanc:1,issu:3,iter:3,key1:1,key2:1,known:2,latest:3,learn:4,leav:1,leukemia:5,level:[0,1],like:1,list_of_gene_nam:1,load_featur:0,louvain:4,make:3,marker:2,matplotlib:1,matrix:1,memori:1,method:2,methyl:3,might:2,miniconda:4,miniconda_:4,modul:[],moignard15:2,more:1,most:1,multi:2,n_ob:1,n_var:1,name:1,natur:5,neighbor:3,none:1,normal:0,note:[3,6],numba:4,numer:1,object:1,obs:1,obs_nam:1,observ:1,offer:2,oper:1,other:3,out:1,paga:2,page:[],panda:1,pass:1,paul15:2,pbmc:2,per:0,phenotyp:5,pip3:4,pip:[3,4],pipelin:1,plot:[0,1],plotting_param:1,possibl:1,post:1,preprocess:2,procedur:3,provid:[1,2],pseudotim:2,pull:4,pypi:4,python:4,qualiti:0,ranger:2,read:1,read_csv:1,readm:3,readthedoc:3,recip:0,recommend:2,refer:2,reimplement:2,releas:[3,6],report:3,research:3,resolut:2,respect:1,result:2,retriev:1,reveal:5,rna:3,run:4,satija15:2,scanpi:[0,1,2,3,4,6],scanpy_:3,scikit:4,seaborn:4,search:3,see:[0,1,3,4,6],sentenc:3,set:1,seurat:2,sever:2,should:3,show:1,simpl:2,singl:5,slice:1,soon:3,spars:3,start:2,statsmodel:4,still:3,store:1,subsequ:1,techniqu:3,thi:[1,2],time:1,too:3,tool:1,tool_param:1,toolkit:3,trajectori:2,transit:1,tsne:1,two:2,type:[1,2],typic:1,unchang:1,uns:1,unstructur:1,use:[1,3],useful:3,using:[1,2,4],valu:1,var_nam:1,variabl:[0,1],veloc:3,via:[1,2],visn:5,visual:[0,5],want:1,well:3,when:3,where:1,which:1,whole:[1,2],wolf:3,work:[3,4],would:2,write:1,write_csv:1,write_loom:1,you:[1,2,4],your:3,zheng17:2},titles:["API","Usage Principles","Tutorials","Episcanpy \u2013 Epigenomics single cell analysis in python","Installation","References","Version 0.0.1 <span class=\"small\">January 17, 2019</span>"],titleterms:{anaconda:4,analysi:3,anndata:1,api:0,atac:2,basic:0,cell:[2,3],document:[],epigenom:3,episcanpi:3,indic:[],instal:4,januari:[3,6],methyl:2,preprocess:0,principl:1,python:3,refer:5,singl:[2,3],tabl:[],tutori:2,usag:1,version:[3,6],welcom:[],workflow:1}})