ISMARA client

ISMARA client preprocesses raw RNA-seq and ChIP-seq NGS datasets locally to generate compact summary files for ISMARA (Integrated System for Motif Activity Response Analysis) motif activity and regulatory inference.

Key Features:

• Local Data Pre-Processing: Performs local pre-processing of raw RNA-seq and ChIP-seq data to produce compact summary files and can reduce data size by up to a factor of 1000.
• Efficient Data Transfer: Produces small summary files that minimize upload size and can reduce upload time from hours to seconds when transferring to the ISMARA server.
• Privacy Considerations: Keeps raw NGS datasets local and uploads only essential summary files to mitigate data confidentiality concerns for proprietary datasets.
• Automated Workflow Integration: Automates generation of processed summary files and their subsequent upload to the ISMARA server to integrate with ISMARA analyses.

Scientific Applications:

• Regulatory Inference: Enables inference of key regulators, motif activities, and regulatory interactions from high-throughput gene expression and chromatin state datasets.
• Preprocessing for ISMARA Analyses: Prepares large NGS datasets (RNA-seq, ChIP-seq) for downstream motif activity response analysis on the ISMARA server by providing compact, analysis-ready summary files.

Methodology:

Performs local, computation-intensive pre-processing of raw RNA-seq and ChIP-seq NGS data to produce compact summary files that encapsulate information required for downstream analysis on the ISMARA server.