ChIP-Seq
Avadis NGS supports a workflow for the analysis and visualization of ChIP-Seq data. The workflow provides the ability to identify transcription factor binding sites and histone modification sites using the PICS and MACS peak detection algorithms. It supports the ability to detect motifs in the peak regions, and scan for known motifs in the genome or region of interest. Further downstream analysis such as GO, pathway analysis, etc can be performed on the set of affected genes.
Download the ChIP-Seq Highlights Guide
Watch the ChIP-Seq Webinar Recording
Peak Detection
Identify protein binding sites using two peak finding algorithms, PICS and MACS. View the results in the Genome Browser in the context of known genes.
Discover Significant Motifs
Discover the most significant motifs present in the vicinity of the binding regions using an efficient implementation of the GADEM algorithm. Motifs in JASPAR format can be imported and occurrences of the motifs can be detected by scanning the whole genome.
Affected Genes
Identify genes affected by transcription factor regulation.
GO Analysis
Perform GO analysis to identify significant GO terms for affected genes.
Pathway Analysis
Use the packaged database of 2 million interactions (with supporting PubMed references) to find relationships between genes.
Compare gene lists
Compare different gene lists from multiple experiments and across organisms.
