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CACIMAR (version 1.0.0)

Cross-Species Analysis of Cell Identities, Markers and Regulations

Description

A toolkit to perform cross-species analysis based on scRNA-seq data. This package contains 5 main features. (1) identify Markers in each cluster. (2) Cell type annotation (3) identify conserved markers. (4) identify conserved cell types. (5) identify conserved modules of regulatory networks.

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Version

Install

install.packages('CACIMAR')

Monthly Downloads

199

Version

1.0.0

License

MIT + file LICENSE

Issues

10

Pull Requests

0

Stars

12

Forks

6

Maintainer

Junyao Jiang

Last Published

May 18th, 2022

Functions in CACIMAR (1.0.0)

OrthG_Hs_Zf

Orthologs genes database for homo sapiens and zebrafish
Plot_MarkersHeatmap

Plot Markers in each cell type
Identify_ConservedMarkers

Identify orthologs marker genes for two species
OrthG_Zf_Ch

Orthologs genes database for mus zebrafish and chicken
OrthG_Mm_Zf

Orthologs genes database for mus musculus and zebrafish
OrthG_Mm_Ch

Orthologs genes database for mus musculus and chicken
Format_Markers_Frac

Format marker genes for plotting
Identify_ConservedCellTypes

Identify conserved cell types based on power of genes and orthologs database
CACIMAR_cols

CACIMAR colors palette
Identify_Markers

Identify markers of each cluster
OrthG_Hs_Ch

Orthologs genes database for homo sapiens and zebrafish
Heatmap_Cor

plot the heatmap of marker genes across different species
Identify_ConservedNetworks

Identify conserved regulatory networks
OrthG_Hs_Mm

Orthologs genes database for homo sapiens and mus musculus
Identify_CellType

Identify cell type of each cluster