RBPBench is a multi-function tool to evaluate CLIP-seq and other related genomic region data using a comprehensive collection of known RNA-binding protein (RBP) binding motifs. RBPBench can be used for a variety of purposes, from RBP motif search (database or user-supplied RBP motifs) in genomic regions, over motif enrichment and co-occurrence analysis, in-depth comparisons over multiple datasets via sequence and genomic annotation statistics, to benchmarking CLIP-seq peak caller methods as well as comparisons across cell types and CLIP-seq protocols. RBPBench supports both sequence and structure motifs, as well as regular expressions (sequence and structure patterns). Moreover, users can easily provide their own motif collections.

MIT

RepEnrich

Sequence analysis

Tool

RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.

Python

Other