L1kprocs an r package for l1000 data processing and analysis
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L1KProcs: an R package for L1000 data processing and analysis. Chenglin Liu , Kun Wei and Jing Su Center for Bioinformatics and Systems Biology Wake Forest School of Medicine. Overview. L1KProcs.

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L1KProcs: an R package for L1000 data processing and analysis

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L1kprocs an r package for l1000 data processing and analysis

L1KProcs: an R package for L1000 data processing and analysis

Chenglin Liu , Kun Wei and Jing Su

Center for Bioinformatics and Systems Biology

Wake Forest School of Medicine


Overview

Overview


L1kprocs

L1KProcs

  • L1KProcs is an R package and interface for LINCS L1000 data preprocessing and compound signature detection in both text-mode and graphic-mode way.

  • Additionally, it is a library for existing L1000 processed expression data and their connections (EGEM library).


L1kprocs1

L1KProcs

  • Operating system:

    • Windows XP, Windows 7, Linux, Mac OS X

  • Open source

    • R language based (R>=3.0)

  • Parallel computing

    • Require doParallel package

  • Access

    • download, web


Function i preprocessing

Function I: preprocessing


How to use

How to Use

  • Required Input: the location of raw L1000 data

  • Optional Input:

    • target: quantile normalization

    • ifAll: if convert the landmark gene expression to whole genome data

    • nthread: number of parallel computing

    • plot: data quality visualization

  • Output:

    • The processed data saved in outpath.

    • The information of the data including the qualities and the control wells in class listlstPlateInfo.


Data quality visualization

data quality visualization


Single well peak calling and visualization

Single well peak calling and visualization


Function ii egem matrix

Function II: EGEM matrix

  • Required Input

    • cpdata: LFC after compound treatments

  • Optional Input

    • LINCS:

      • if TRUE, specify the name of the existing EGEM library lib.name

      • otherwise, provide the LFC after knockdown treatments

    • nthread: number of parallel computing

  • Output

    • The EGEM matrix and annotations


Function ii egem matrix1

Function II: EGEM matrix


Function iii compoun d signature discovery

Function III: Compound Signature Discovery

  • Required Input

    • The output of Function II egem.info.

    • The range of signature number pNo.

  • Optional Input

    • nthread: number of parallel computing

  • Output:

    • Signature number k

    • Compounds and signature genes.


Function iii compound signature discovery

Function III: Compound Signature Discovery


L1kprocs interface

L1KProcs Interface


L1000 preprocessing

L1000 preprocessing

Choose one

raw L1000 data

Upload and

start computing


Compound signature discovery

Compound Signature Discovery

nthread

  • start computing


Single well peak calling visualization

Single well peak calling visualization


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