Usage

The fields are shown in the help.

$ python run_cyclum.py --help
usage: run_cyclum.py [-h] [--cell-is-column] [--no-transform] [--remove]
                     [--binary-output] [--binary-output-only] [--linear q]
                     input [output]

Recover and remove cell cycle.

positional arguments:
  input                 input file name
  output                output name mask; the prefix for all output names

optional arguments:
  -h, --help            show this help message and exit
  --cell-is-column      indicating that each column represents a cells
  --no-transform        indicating that no further transform is needed
  --remove              also output the cell cycle removed expression matrix
  --binary-output       output using binary file; faster to read by python or
                     R
  --binary-output-only  output using binary file only without csv
  --linear q            integer number of linear dimensions

Arguments	Annotation
input	The full name of the input file (tab delimited with cell names and gene names. The names do not have to have a meaning.)
output	The prefix of outputs. Default to be the prefix of input
--cell-is-column	Tell the program that each column (i.e. not row) stands for a cell
--no-transform	Tell the program not to log transform the imput data
--remove	Besides the cell timings and gene profiles, also output the cell cycle removed expression matrix
--binary-only	output using binary file only (without csv)
--linear q	q is an integer, the number of linear dimensions

The output file names will be the output prefix trailed by “-cell.csv”, “-gene.csv” and “-corrected.csv”.