README.md

In effiken/scDissector: Exploratory Data Analysis tool for single-cell RNA-seq data

Installation

1. Install R (in case you don't have it already installed):

   Download and install R.

   You may want to install RStudio as well.

2. Install devtools package in R (in case you don't have it already installed):

   install.packages("devtools")

   library(devtools)

3. Install scDissector:

   install_github("effiken/scDissector")

Update

1. Load devtools

library(devtools)

1. Install the package as in (3) above

Running scDissector in R

library(scDissector)

run_scDissector()

or

run_scDissector(clustering_data_path =**["PATH"]**)

Loading the data prior to running scDissector

Loading the data prior to running scDissector is recommended:

ldm = load_scDissector_data(clustering_data_path=**["PATH"]**, model_name=[STRING], sample_names=[VECTOR_OF_STRINGS])

run_scDissector(preloaded_data = ldm, clustering_data_path = **["PATH"]**)

Loading Seurat Object and running scDissector

ldm=load_seurat_rds("[seurat_rds_file_path]",model_name,clustering_data_path=**["PATH"]**)

run_scDissector(preloaded_data = ldm, clustering_data_path = **["PATH"]**)

Loading MetcCell Object and running scDissector

ldm=load_metacell_clustering(mc_file,mat_file,model_name,clustering_data_path=["PATH"])`

run_scDissector(preloaded_data = ldm, clustering_data_path = **["PATH"]**)

scDissector-powered websites

https://scDissector.org/martin (Martin et al. Cell 2019)

effiken/scDissector documentation built on July 28, 2023, 6:08 a.m.