BioWinfordSC Platform
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singlecell.zip
spatial_data1.zip
spatial_data2.zip
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Spatial
QC
Reduction
FindMarker
SingleR
scMayoMap
T-CellAnnoTator
sc_DEG
Expression
monocle2
monocle3
CellChat
CellPhone
CellTalker
inferCNV
CopyKat
scWGCNA
scGSEA
AUCell
scMetabolism
ScregClust
SCENIC
scTenifoldKnk
Scissor
BayesPrism
User Guide
upload (<200MB)
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specify the clusters
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specify the celltypes (;)
Run
upload (<200MB)
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min count of genes
max count of genes
min count of RNAs
max count of RNAs
max percent.mt
enable Harmony
FALSE
TRUE
Run
dims:
auto
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resolution:
specify the clusters
All
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condition
Browse...
Run
logFC:
method
wilcox
bimod
t
roc
poisson
DESeq2
MAST
Run
Reference
Hematopoietic
Human_all
Monaco_114s
Mouse_all
Mouse_imm
Custom Celltype
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Run
Tissue
NULL
adipose tissue
bladder
blood
bone
bone marrow
brain
breast
embryo
eye
gastrointestinal tract
heart
kidney
liver
lung
mammary gland
muscle
other
ovary
pancreas
placenta
prostate
skin
spleen
stomach
testis
thymus
tooth
uterus
Custom Celltype
Browse...
Run
Custom Celltype
Browse...
Run
logFC:
bygroup
cluster
celltype
group
celltype1
celltype2
condition
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switch the case & control
no
yes
Run
type
seurat_clusters
celltype
group
cell/sample group
Browse...
Run
genes (g1,g2)
specify cells (c1,c2)
num_dim
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fix sample effect
FALSE
TRUE
Run
genes (g1,g2)
specify cells (c1,c2)
Run
Group
source cells(;)
target cells(;)
layout
circle
hierarchy
chord
heatmap
search
Secreted Signaling
Cell-Cell Contact
ECM-Receptor
Run
Group
source cells(;)
target cells(;)
Run
Group
top genes to show
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color choice
nature_palette
lancet_palette
jama_palette
Run
ref cells(a,b)
Run
ref cells(a,b)
n_subpop
2
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Run
group name
condition
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minModuleSize
Run
gene name(option1)
condition(option2)
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upload GMT
Browse...
Run
upload GMT
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Run
pathway list
Browse...
group
Run
cell type
group
penalization
0.1
0.15
0.2
0.25
0.3
0.35
0.4
0.45
0.5
Run
celltypes(;)
groups(;)
topN regulons
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Species
Human
Mouse
Run
cell type
group
knockout_genes(;)
genes to show
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Only keep HVGs
YES
NO
Run
family
binomial
cox
alpha
0.005
0.01
0.05
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
cutoff
0.1
0.15
0.2
0.25
0.3
0.35
0.4
0.45
0.5
Run
Species
hs
mm
Run