Categories
Organoid: SPRING embedding
Organoid: tSNE clusters
Organoid: Pseudotime pattern
Organoid: scATAC-seq
Primary adult: tSNE
Primary adult: dotplots
Primary adult: layer
Data categories
Human full trajectory
Human 2M organoids
Human & Chimp full trajectory
Human & Chimp & Macaque 2-4M organoids
Parameter settings:
Number of panels:
One
Two
Information to show:
Gene
Metadata
Gene:
Metadata:
Line
Stage
Constrains (line):
H9
409b2
Constrains (stage):
iPSCs
EB
Neuroectoderm
Neuroepithelium
1M organoid
2M organoid
4M organoid
Information to show:
Gene
Metadata
Gene:
Metadata:
Line
Stage
Constrains (line):
H9
409b2
Constrains (stage):
iPSCs
EB
Neuroectoderm
Neuroepithelium
1M organoid
2M organoid
4M organoid
Plot output:
Parameter settings: [scroll down for the plots]
Number of panels:
One
Two
Information to show:
Gene
Metadata
Gene:
Metadata:
Line
Lineage
Cell type
Pseudotime
Constrains (line):
409b2
H9
Wibj2
Sc102a1
Kucg2
Sojd3
Hoik1
Constrains (lineage):
Dorsal forebrain
Ventral forebrain
Non-forebrain
Information to show:
Gene
Metadata
Gene:
Metadata:
Line
Lineage
Cell type
Pseudotime
Constrains (line):
409b2
H9
Wibj2
Sc102a1
Kucg2
Sojd3
Hoik1
Constrains (lineage):
Dorsal forebrain
Ventral forebrain
Non-forebrain
Plot output:
Parameter settings:
Information to show:
Gene
Metadata
Gene:
Metadata:
Line
Stage
Constrains (line):
H9
409b2
SandraA
Constrains (stage):
iPSCs
EB
Neuroectoderm
Neuroepithelium
1M organoid
2M organoid
3M organoid
4M organoid
Plot output:
Parameter settings:
Information to show:
Gene
Metadata
Gene:
Metadata:
Stage
Pseudotime
Aligned pseudotime
Mask the non-cortical data
Mask the unaligned data
Show macaque data
Plot output:
Data categories
Human full trajectory
Chimp full trajectory
Gene:
Clusters:
Plot output:
Gene:
Clusters:
Plot output:
Data categories
Human 2M organoids
Human & Chimp & Macaque 2-4M organoids
Parameter settings:
Mode
Multiple genes
One gene in lines
Gene:
Genes:
Show raw data points
Plot output:
Parameter settings:
Genes:
Show raw data points
Show the aligned pseudotimes
Plot output:
Data categories
Human full trajectory
Human-Chimp DA in organoids
Parameter settings:
Information to show:
Peak
Enrichment
Gene:
Show raw data points
Constrains:
Promoter peaks
Enhancer peaks
Peak:
Feature:
Plot output:
Parameter settings:
Gene:
Only show DA peaks
Constrains:
Promoter peaks
Enhancer peaks
Peak:
Show data before coverage normalization
Plot output:
Information to show:
Gene
Metadata
Gene:
Metadata:
Species
Segment
Sample layer index
Species:
Human
Chimp/Bonobo
Macaque
Clusters:
Plot output:
Genes:
Plot output:
Parameter settings:
Gene:
Neuron subtypes:
Excitatory neuron
Inhibitory neuron
Plot output:
