NGDC BIT

Category

Visualization

Bar Box Comutation Dot Forest Heatmap Histogram Lollipop Mafsummary Maftitv Manhattan Oncoprint PM-Adiversity PM-comp-cor PM-comp-func PM-comp-taxa PM-Distribution PM-Hcluster PM-Heatmap PM-Marker-Corr PM-Marker-RFscore PM-Marker-Test PM-Network PM-Pca PM-Pcoa PM-plot-taxa PM-rare-curv Q-Q Survival Upset Venn

Sequence alignment

BLAST Dotmatcher Dotpath Dottup Needle PM-Bdiversity PM-extract-rna PM-parallel-meta PM-pipeline PM-profiler Polydot Water

RNA Expression

Bulk RNA-seq Data Analysis Cancer Alternative Splicing Analysis CCLHunter CIRI-deep CIRI3 Cross-disease analysis Disease prediction Editing site annotation Editing site identification EFDetector FunGen Gene-disease network construction HELIX NCSelPred RNA-seq Analysis Single-cell RNA-seq Data Analysis SPIRAL TIVar diff TIVar predict Visualization of scRNA-seq Data Analysis Results

Variome analysis

BarcodeBLAST BarcodeFinder easyGWAS ExpPattern GeneFinder Haplotype analysis HapMap HapSnap LeadSNPFinder Pangolin LOCATOR Rice Varieties Identification Rice Yield Estimation SeqFetch VersionMap Wheat Head Estimation

Epigenome analysis

Age Predictor BS-RNA Comparative analysis in nucleosomes DMR Annotation DMR Toolkit Enrichment & Annotation Enrichment analysis in nucleosome occupancy EWAS Network Visualization GMQN IDMP Lollipop Plotter MRAS

Long non-coding RNA

Classification Functional Prediction ID conversion LGC lncbook-BLAST LncBot

Virus

COVID-19 genome variation annotation COVID-19 haplotype analysis Denovo Assembly Evolutionary tree Fastq-to-Variants Genealogy and Evolutionary Analysis Genome Annotation Genome Tracing InfluProto McAN Monkeypox virus genome variation annotation Monkeypox virus genome variation identification Pangolin COVID-19 Lineage Assigner SeqQC VENAS VISTA

Single-cell omics

Cell Type Comparator Cell Type Predictor FGOT GOT MultiChat RegChat SCSES SpaDC spaDIVA SpaMI TACOS

Image Processing

Image Cropping Image Denoising Image Flipping Image Partitioning Image Resizing

Others

Composition analysis Cross-model analysis Cross-species analysis Cross-stages analysis Homolog Finder LUTLSRS MEFE MIA Microbiome Search Engine MT-tracker ncRNA-eQTL PM-parse-mip PM-predict-func PM-predict-func-contribute PM-predict-func-nsti PM-rand-rare PM-select-func PM-select-taxa PM-split-seq TaxaCal

Category

User Manual Sign in

Single-cell omics

SCSES GOT SpaMI FGOT TACOS RegChat SpaDC spaDIVA MultiChat Cell Type Comparator Cell Type Predictor

Home / Single-cell omics / MultiChat

Tool Configuration

Spatial Cell-Cell Communication

File Type

MultiChat

MultiChat

Data

RNA expression matrix*

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

Cell annotations*

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

Spatial coordinates*

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

Ligand-receptor database*

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

Cell embedding

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

LR-TF-TG path database

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

ATAC matrix

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

Peak-gene links

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

Peak-TF matrix

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

Gene embedding

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

TF embedding

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

Peak embedding

Input data text

Upload a file

Upload a file

This data field is required. Please enter text or upload a file.

Parameters

Analysis mode

lrs

lrs

rna-paths

atac-prepared

Align

strict

strict

intersection

Normalize log

False

True

False

Aggregation

mean

mean

median

Volatile method

mad

mad

median

ratio

Device

cpu

cpu

cuda

Invert y

False

True

False

Path axis

ligand

ligand

tg

both

Path significance

True

True

False

Cell type column

Lr

Weight decay

Attention dropout

Contrastive temperature

Relative tolerance

Alpha

Volatile threshold

Point size

Path volatile threshold

Minimum expressing cells per gene

Smooth k

Neighbors

Positive cells

Epochs

Background epochs

Contrastive projection dimensions

Early stop after

Background runs

Background positive cells

Background seed

Min cells count

Seed

Gpu id

Threads

Log every

Plot top

Path components

References

Instructions

Spatial Cell-Cell Communication

MultiChat uses heterogeneous graph modeling to jointly embed distinct signaling components and infer signaling cascades mediated by ligand–receptor pairs.

Contributor(s)

cwzhen@whu.edu.cn

Result Preview

Example output and submitted task results are displayed here.

#Runs 9

Open result Download result