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CL_Expect, v59

Predicts which cell lines should get removed at various points in the Achilles pipeline.

Author: Ann Sizemore;Broad Institute

Contact: AchillesTeamArchive@gmail.com

Algorithm Version:

Introduction

[Why use this module? What does it do? If this is one of a set of modules, how does this module fit in the set?]

Algorithm

[if applicable: a short overview of the algorithm in normal prose, followed by any details; write overview as if you are explaining to a novice]

References

[appropriate papers cited]

Parameters

Name Description
gct file * Initial gct file after filterLowPert
removelist * Remove list (annotation file for removeSamples)
sample info file * Sample info file (annotation file for collapseReps)
cn segtab * Copy number seg.txt file (annotation file for CN_Cutoff)
CN file * Copy number variants file (annotation file for PertCNFilter)
keep list  List of lines to keep (from KeepSamples).

* - required

Input Files

  1. [parameter name]
    [Description. For example: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the GenePattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.

Output Files

  1. [File name]
    [Description of the content, file format, and how to interpret the results.]

Example Data

[provide example data, including input files and parameter settings]. (we’ll put the input files on the ftp site and link to them from the doc)

Requirements

[any software requirements for running this, e.g., version of R, licensing]

Platform Dependencies

Task Type:

CPU Type:
any

Operating System:
any

Language:
any

Version Comments

Version Release Date Description
59