Htsint: a Python library for sequencing pipelines that combines data through gene set generation.

ABSTRACT:

Background

Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses.

Results

We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation

SUBMITTER: Richards AJ 

PROVIDER: S-EPMC4581156 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature