CHIPSTER

chipster screenshot

 

Chipster is a Java-based application for analysis of high-throughput biological data. It provide user-friendly graphical interface for running most popular tools for microarray and high-throughput sequencing data analysis. Due to convenient organization of the working space, the data analysis and visualization is clear and straightforward. All computations are calculated using the PLGrid infrastructure.

The user guide, including tutorials is available on PLGrid Documentation page.

 

Main features

On our instance we provide access to a limited set of build-in genomes (16 at the moment) but additional reference information can be incorporated by user. The set of available tools include:

  • NGS pre-processing tools:
    • FastQC
    • fastx toolkit
    • Trimmomatic
    • PRINSEQ
  • Data manipulation tools:
    • bedtools
    • samtools
  • Microarray analysis:
    • Normalization and preprocessing
    • Annotation
    • Differential expression
    • miRNA analysis including miRNA targets
    • Supported arrays: Illumina, Affymetrix, Agilent
  • NGS Mapping tools:
    • bowtie 1&2
    • Tophat2
    • BWA
  • Sequence analysis:
    • BLAST
    • MAFFT
    • PRIMER3
    • Alignment visualization and analysis tools
  • Others:
    • format converters
    • visualization tools
    • text file manipulation tools
    • and many others
  • RNA-seq tools:
    • Tophat-Cufflinks-Cuffdiff suite
    • miRNA profiling
    • htseq
    • DEXseq
    • DEseq
    • edgeR
    • ChIP-Seq tools:
    • F-seq
    • MACS2

Only 3 steps to use the Chipster services

l
1. Register to PL-GRID: link
N
2. Apply to biology services: documentation
I
4. Run Chipster and enjoy

Documentation

PL-Grid NG:

Biological services in PL-GRID NG documentation:

Please refer to the Chipster for the detailed documentation on the Chipster itself.