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1Job name(optional)
2Expression matrix
A matrix of data containing gene expression, with rows for genes and columns for cells.
Example
The file format is limited to rds and size is limited to 600M.
3Cell metadata
Contains metadata information about each cell, such as cell type, experimental conditions, etc.
Example
The file format is limited to rds and size is limited to 600M.
4Gene metadata
Contains metadata information about each gene, such as gene name, gene function, etc.
Example
The file format is limited to rds and size is limited to 600M.
5Dimensionality reduction method
6Label for mapping classification
Monocle3
Introduction
Monocle 3 is a popular computational tool for analyzing single-cell RNA sequencing data and reconstructing cell development tracks. By analyzing single-cell RNA sequencing data, we can infer the developmental trajectory and differentiation path between cells, and identify the key states and transition points of cells during development, thereby revealing the molecular mechanisms of cell fate decision making and cell type transformation.
Demo data
When running demo data;
expression matrix file: packer_embryo_expression.rds;
cell metadata file: packer_embryo_colData.rds;
gene metadata information file: packer_embryo_rowData.rds;
dimension reduction method: UMAP;
mapping classification label: cell.type;
Result
The output results are:
- out.rds:The result is retained as an rds file
- dim_reduction.png:Dimensionality reduction graph
- clustering. png:clustering diagram
- trajectory.png:trajectory inference diagram
- Pseudotime. png:pseudotime analysis chart