/single-cell-IMP-methods

A set of wrappers for single-cell RNA-seq imputation methods.

Primary LanguageShell

single-cell-IMP-methods

Running

Command to run each algorithm:

# scImpute
./run_scripts/scimpute.sh input_file.csv output_file.csv output_dir
# MAGIC
./run_scripts/magic.sh input_file.csv output_file.csv output_dir
# UNCURL
./run_scripts/uncurl.sh input_file.csv output_file.csv output_dir
# BISCUIT (is very buggy)
./run_scripts/uncurl.sh input_file.csv output_file.csv output_dir
# DCA (cpu version only)
./run_scripts/dca-cpu.sh input_file.csv output_file.csv output_dir
# DECODE (needs verification)
./run_scripts/decode.sh input_file.csv output_file.csv output_dir
# DrImpute
./run_scripts/drimpute.sh input_file.csv output_file.csv output_dir
# kNN-smoothing
./run_scripts/knn-smoothing.sh input_file.csv output_file.csv output_dir

Re-Building

There is no need to build images locally. However, To build docker images run:

./build_all.sh