cellbrowser.conf

# --------- REQUIRED SETTINGS --------------

# example config file with all possible settings
# For a minimal file, see minimal.conf

# internal short name, only visible in the URL
# same as the output directory name
# no special chars, no whitespace, please
name = "sample"

# priority determines the order of the datasets
# smallest comes first
priority = 10

# tags are shown in the dataset browser
# current tags:
# smartseq2,10x
tags = ["smartseq2"]

# human-readable name of this dataset
shortLabel="CellBrowser 100-genes demo"

# name of the expression matrix file, genes are rows
exprMatrix="exprMatrix.tsv.gz"

# "gencode22", "gencode23", "gencode24", etc or "symbol"
# For "symbol" you can specify which database to use to check
# symbols or, for cbHub, how to map them to the genome.
#geneIdType="symbol"
geneIdType="symbol/gencode24"

# name of the meta data table ("samplesheet). One sample per row. First row is name of sample.
meta="meta.tsv"

# we try to auto-detect the field type of fields in the meta data.
# Sometimes, this doesn't work, e.g. when your cluster ID is a numer
# or your C1 chip ID is a number, but you don't want them binned, you want
# to treat as if they were categories
enumFields = ["c1_cell_id"]

# tsv files with coordinates of every sample in format <sampleId, x, y>
# first the name of the file, then a human readable description
coords=[
    {"file":"tsne.coords.tsv", "shortLabel":"t-SNE on WGCNA"},
]

# --------- OPTIONAL SETTINGS --------------

# default field in the meta data table with the name of the cluster
clusterField="WGCNAcluster"

# default field in the meta data table used for the label of the clusters shown by default
labelField="WGCNAcluster"

# tsv files with marker gene lists for the clusters 
# format is (clusterName, geneSymbol, pValue, enrichment) + any additional fields or URLs you want to show
#markers=[
    #{"file":"markers.tsv", "shortLabel":"Cluster-specific markers"}
#]

# optional: UCSC track hub with the BAM file reads and expression values 
hubUrl="http://cells.ucsc.edu/cortex-dev/hub/hub.txt"

# optional: table with <name><color> for any meta data values
# color is a six-digit hexcode
# name is a any value in the meta data table
colors="colors.tsv"

# should the cluster labels be shown by default (default: true)
showLabels=True

radius = 5
alpha = 0.3

acroFname = "acronyms.tsv"

quickGenesFile = "quickGenes.csv"

# --- The following options are only used by cbHub ---
hubName = "100 Genes Sample Hub" # name of hub (optional, default is value of 'shortLabel')
ucscDb = "hg38" # UCSC genome ID of the BAM files, required
bamDir = "bam" # directory with .bam files, optional. If not present, don't do bam merging
#clusterOrder = "clusterOrder.txt"  # file with cluster names in order (default is alphabetical)
unit = "TPM"   # any string, shown on genome browser, the unit of the values in the matrix