@xysheep xysheep released this Mar 24, 2018 · 1 commit to master since this release

Assets 3

Update

  • Fix a bug that argument "cofactor" conflicts with some old arguments.
  • Fix a broken test data file

Quick Start

Before run the executable, you need to first install MATLAB Runtime 9.2 avaliable at https://www.mathworks.com/products/compiler/matlab-runtime.html.

You can test C2G.exe with provided example. In this example, "data.csv" is a n-by-m data matrix without header where n is number of cells and m is number of markers. "label.csv" is a 10 k-means defined clustering results. In label.csv, each row is one single number corresponding to clustering assignment of one cell in data.csv.

C2G.exe data.csv label.csv

If the your data is not transformed, you also need to set the "cofactor" option to make C2G transform the data. For mass cytometry, it's recommended to be 5. For flow cytometry, it's recommended to be 100.

C2G.exe data.csv label.csv cofactor 5

Usage

C2G.exe datafile clusterfile [...options]

Required Arguments:

  datafile: Path to a CSV file of data matrix. This file should have a
          n-by-m matrix without header. n is the number of cells and
          m is number of markers. This data should already be
          compensated and transformed, otherwise, need to use "cofactor" 
          option to transform them.
  clusterfile: Path a CSV file of cluster labels. This file
          should have a n-by-1 matrix without header. n is the number
          of cells. Each row correspondong to one cell in datafile. 0
          means unlabeled.

Optional Arguments:

Details of optional arguments are avaliable at https://github.com/xysheep/C2G

@xysheep xysheep released this Feb 23, 2018 · 1 commit to master since this release

Assets 3

Update

  • Fix a bug that argument "cofactor" conflicts with some old arguments.

Quick Start

Before run the executable, you need to first install MATLAB Runtime 9.2 avaliable at https://www.mathworks.com/products/compiler/matlab-runtime.html.

You can test C2G.exe with provided example. In this example, "data.csv" is a n-by-m data matrix without header where n is number of cells and m is number of markers. "label.csv" is a 10 k-means defined clustering results. In label.csv, each row is one single number corresponding to clustering assignment of one cell in data.csv.

C2G.exe data.csv label.csv

If the your data is not transformed, you also need to set the "cofactor" option to make C2G transform the data. For mass cytometry, it's recommended to be 5. For flow cytometry, it's recommended to be 100.

C2G.exe data.csv label.csv cofactor 5

Usage

C2G.exe datafile clusterfile [...options]

Required Arguments:

  datafile: Path to a CSV file of data matrix. This file should have a
          n-by-m matrix without header. n is the number of cells and
          m is number of markers. This data should already be
          compensated and transformed, otherwise, need to use "cofactor" 
          option to transform them.
  clusterfile: Path a CSV file of cluster labels. This file
          should have a n-by-1 matrix without header. n is the number
          of cells. Each row correspondong to one cell in datafile. 0
          means unlabeled.

Optional Arguments:

Details of optional arguments are avaliable at https://github.com/xysheep/C2G

@xysheep xysheep released this Jan 25, 2018 · 13 commits to master since this release

Assets 3

Update

  • Support transformation of the data in compiled version of C2G

Quick Start

Before run the executable, you need to first install MATLAB Runtime 9.2 avaliable at https://www.mathworks.com/products/compiler/matlab-runtime.html.

You can test C2G.exe with provided example. In this example, "data.csv" is a n-by-m data matrix without header where n is number of cells and m is number of markers. "label.csv" is a 10 k-means defined clustering results. In label.csv, each row is one single number corresponding to clustering assignment of one cell in data.csv.

C2G.exe data.csv label.csv

If the your data is not transformed, you also need to set the "cofactor" option to make C2G transform the data. For mass cytometry, it's recommended to be 5. For flow cytometry, it's recommended to be 100.

C2G.exe data.csv label.csv cofactor 5

Usage

C2G.exe datafile clusterfile [...options]

Required Arguments:

  datafile: Path to a CSV file of data matrix. This file should have a
          n-by-m matrix without header. n is the number of cells and
          m is number of markers. This data should already be
          compensated and transformed, otherwise, need to use "cofactor" 
          option to transform them.
  clusterfile: Path a CSV file of cluster labels. This file
          should have a n-by-1 matrix without header. n is the number
          of cells. Each row correspondong to one cell in datafile. 0
          means unlabeled.

Optional Arguments:

Details of optional arguments are avaliable at https://github.com/xysheep/C2G

@xysheep xysheep released this Nov 11, 2017 · 27 commits to master since this release

Assets 3

Update

  • Support for user without access to MATLAB
  • Handles outliers better
  • Support all parameters of source version in the executable

Quick Start

Before run the executable, you need to first install MATLAB Runtime 9.2 avaliable at https://www.mathworks.com/products/compiler/matlab-runtime.html.

You can test C2G.exe with provided example. In this example, "data.csv" is a n-by-m data matrix without header where n is number of cells and m is number of markers. "label.csv" is a 10 k-means defined clustering results. In label.csv, each row is one single number corresponding to clustering assignment of one cell in data.csv.

C2G.exe data.csv label.csv

Usage

C2G.exe datafile clusterfile [...options]

Required Arguments:

  datafile: Path to a CSV file of data matrix. This file should have a
          n-by-m matrix without header. n is the number of cells and
          m is number of markers. This data should already be
          compensated and transformed.
  clusterfile: Path a CSV file of cluster labels. This file
          should have a n-by-1 matrix without header. n is the number
          of cells. Each row correspondong to one cell in datafile. 0
          means unlabeled.

Optional Arguments:

Details of optional arguments are avaliable at https://github.com/xysheep/C2G

Nov 11, 2017
Ignore complied files

@xysheep xysheep released this Sep 21, 2017 · 47 commits to master since this release

Assets 2

More Comprehensive Documents and Available Options

@xysheep xysheep released this Aug 8, 2017 · 79 commits to master since this release

Assets 2

In this release, I updated the demo.m and allow the user to see more detail while running C2G.

@xysheep xysheep released this Aug 8, 2017 · 81 commits to master since this release

Assets 2

This is the first official release of C2G on github.