Skip to content

Releases: xysheep/C2G

v1.2.2 Bug fix

24 Mar 21:00
Compare
Choose a tag to compare

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

V1.2.1 Bug fix

23 Feb 12:56
Compare
Choose a tag to compare

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

V1.2.0 Support build-in transformation

25 Jan 00:02
3407f93
Compare
Choose a tag to compare

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

V1.1.1 Support for non-MATLAB users

11 Nov 09:06
Compare
Choose a tag to compare

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

More Comprehensive Documents and Available Options

21 Sep 21:45
Compare
Choose a tag to compare

More Comprehensive Documents and Available Options

C2G update demo

08 Aug 00:21
Compare
Choose a tag to compare

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

C2G first release

08 Aug 00:10
Compare
Choose a tag to compare

This is the first official release of C2G on github.