Re: [Bioc-devel] Reading and storing single cell ATAC data

2016-09-23 Thread Hervé Pagès
, maybe you don't need to go there? -Andrew Message: 3 Date: Fri, 23 Sep 2016 17:37:04 -0400 From: Caleb Lareau To: bioc-devel@r-project.org Subject: [Bioc-devel] Reading and storing single cell ATAC data Message-ID: <83b8a778-4daa-4a16-9da8-22def9ad1...@g.harvard.edu> Content-Type: text/p

Re: [Bioc-devel] Reading and storing single cell ATAC data

2016-09-23 Thread Andrew McDavid
in Bioconductor. But unless you are generating > 1 TB of semi-processed data, maybe you don't need to go there? -Andrew > Message: 3 > Date: Fri, 23 Sep 2016 17:37:04 -0400 > From: Caleb Lareau > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Reading and sto

Re: [Bioc-devel] Reading and storing single cell ATAC data

2016-09-23 Thread Bemis, Kylie
Hi Caleb, Per your question on sparse on-disk matrices: is your experimental data coming in some pre-defined text or binary file format, or are you looking to convert to a new, custom format to take advantage of the sparsity? I need to start working on an on-disk sparse matrix implementation so

[Bioc-devel] Reading and storing single cell ATAC data

2016-09-23 Thread Caleb Lareau
Hi everyone— I’m working with a team that’s generating single cell ATAC data in large amounts and am designing the framework of an S4 object to facilitate analyses in R. I have a couple of high-level questions that I wanted to pose early to hopefully attain some community guidance in the implem