SPACEGERM
Spa
tial
C
aenorhabditis
e
legans
g
ermline
e
xpression of m
R
NA &
m
iRNA
Virtual in-situ hybridization (vISH)
Spatial clustering
Expression profiles
Gene/miRNA name
Plot options
manually set expression range limis
Span to use for smoothing
# gene clusters
Expression measure
CPM
log2(1 + CPM)
log10(1 + CPM)
Row normalization
scaling (z-scores)
centering only
none
Distance metric
1 - Pearson's r
Euclidean distance
Gene list
import gene list
Peak CPM minimum
Export gene table as XLSX
Gene/miRNA names
Expression level
gene level estimates
isoform level estimates
Expression measure
CPM
CPM / cell
Location measure
Relative position [% distal-to-proximal]
Distance to the DTC [
m]
Migration time from the DTC [h]
Samples
N2_mRNA_A1
N2_mRNA_A2
N2_mRNA_A3
N2_mRNA_P1
N2_mRNA_P2
N2_mRNA_P3
N2_sRNA_A1
N2_sRNA_A2
N2_sRNA_A3
N2_sRNA_P1
N2_sRNA_P2
gld-2_gld-1_mRNA_A1
gld-2_gld-1_mRNA_A2
gld-2_gld-1_mRNA_P1
gld-2_gld-1_mRNA_P2
glp-1_gf_mRNA_A1
glp-1_gf_mRNA_A2
glp-1_gf_mRNA_P1
glp-1_gf_mRNA_P2
Plot options
show raw data points
show raw data lines
show per-sample smooth fits (LOESS)
show across-sample smooth fit (LOESS)
scale y-axis logarithmically (log2)
fix x-axis limits
use single y-scale for all sub-plots
manually set expression range limits
show slice width bars
show gonad arm model (if single column & fixed x-axis limits)
show smoothing standard error
show dropout slices (<10K pseudoaligned reads)
# plot columns
# points to impute for smoothing
Span to use for smoothing