----open_sites_0.01.txt: DNA hypersensitive sites that were accessible in at least 1% of cells in each cluster were used as input to the Cicero. This file is tabular with following columns:
site: coordinates of the accessible sites in UCSC format merged by ‘_’

num_cells_expressed: number cells that had had at least one read overlapping this site

fraction_cells_expressed: fraction of cells that had at least one read overlapping this site relative to all the cells in that cluster

cluster and subset_cluster: as described in all other files?
subcluster: cluster and subset_cluster merged by ‘_’


----open_sites_0.01.rds
the same file as open_sites_0.01.txt but in rds format, to be easily loaded in R
open_sites_0.01 = readRDS('open_sites_0.01.rds’)


----master_cicero_conns.txt
cicero contact matrix for each cluster. Cicero was ran on sites that were open in at least 1% of cells in each cluster. Cicero maps are merged in this files. This file is tabular with following columns:
connection: pair of sites that were co-accessible inferred by Cicero. coordinates are in UCSC format merged by ‘_’ for simplicity. 

Peak1: coordinates of the first site
Peak2: coordinates of the second site


coaccess:cicero coaccessibility score (Pliner, et al. enclosed). sites with co-accessibility > 0.2 are listed in this file.

peak1.isproximal: Peak1 is proximal if it has overlap with 5kb upstream and 1kb downstream of any tss. if this site is proximal, this column is `Yes`
peak1.tss.gene_name: name of the proximal gene overlapping Peak1
peak1.tss.gene_id: Ensemble gene id of the proximal gene gene overlapping Peak1

peak2.isproximal, peak2.tss.gene_name, peak2.tss.gene_id: same as the columns for Peak1

conn_type: connection type between these two sites which can be one of these three types: proximal_proximal, distal_proximal, distal_distal

cluster: Cluster assignment in initial t-SNE
subset_cluster: Cluster assignment in iterative t-SNE space.
subcluster: cluster and subset_cluster merged by ‘_’

----master_cicero_conns.rds: same as master_cicero_conns.txt but in a compressed format to be loaded easily in R.