htSeqTools

htSeqTools provides quality assessment, artifact detection, de novo read-rich region identification, and visualization functions for analysis of ChIP-seq and RNA-seq high-throughput sequencing data.

Key Features:

• Quality assessment: Comprehensive quality assessment of high-throughput sequencing data, including detection of outliers and biases.
• Artifact detection: Identification of inefficient immuno-precipitation artifacts in ChIP-seq and detection of over-amplification artifacts.
• Read-rich region identification: De novo identification of genomic regions with large accumulations of reads.
• Visualization: Visualization of genomic region locations and coverage profiles for interpretation of sequencing results.
• Bioconductor integration: Integration with Bioconductor to leverage its statistical and graphical capabilities.
• Outlier detection and bias correction algorithms: Employs algorithms for outlier detection and bias correction to improve data integrity.

Scientific Applications:

• ChIP-seq Studies: Identification of protein-DNA interactions by supporting high-quality immuno-precipitation, accurate read mapping, and artifact-filtered binding-site refinement.
• RNA-seq Studies: Support for transcriptome analysis through data quality assessment, bias detection, and visualization of gene expression profiles.

Methodology:

Integrates with Bioconductor and employs algorithms for outlier detection and bias correction while producing graphical representations of genomic region location and coverage.