Provides a set of tools for flexible, streamlined, comprehensive cross-linking and immunoprecipitation data analysis. CTK performs preprocessing and mapping of UV cross-linking and immunoprecipitation (CLIP) data, identification of CLIP tag clusters and peak calling, and crosslinking induced mutation site (CIMS) and crosslink-induced truncation sites (CITS) analysis. CTK uses a sparse data representation with reduced memory usage and running time.
Provides a comprehensive analytical suite for RIP-seq analysis, not only including predicting RIP regions with or without a control library but also processing alignments, automatic genomic annotation, visualization from UCSC browser, etc. As an overview, RIPSeeker consists of two major steps: probabilistic inference of RIP regions (HMM posterior decoding and parameter optimization) and significance test for the inferred RIP regions from HMM (Detect RIP regions). RIPSeeker is able to detect strand-specific RIP regions by running the same workflow on either plus and minus strand separately, making use of the strand-specific information retained in the original RIP-seq protocol. It also takes advantage of modern computational architecture equipped with multiple processors by treating each chromosome as an independent thread and computing multiple threads in parallel using mclapply from parallel R package.
Identifies RNA duplexes bound by a specific RNA-binding protein (RBP). hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing.
Allows to study RNA-RNA binding protein (RBP) interactions in human cell lines. PARCLIP_suite maps the sequence reads and calculates the T-to-C conversion frequency for each annotated category of RNA and read length. It permits to inform experimentalists about the quality of their experiments, and the annotation category of their crosslinked RNAs in order to guide downstream data and functional analysis.
Analyses mapped reads from diverse High-throughput sequencing (HTS) experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. Pyicos is a command line utility for the conversion and manipulation of genomic coordinates files. It facilitates HTS analysis through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Pyicos is part of the Pyicoteo suite of tools.
A highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. CLIPSeqTools contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. CLIPSeqTools has applications for a wide range of analyses that will give an in depth view of the analysed dataset. Examples of such analyses are: genome read coverage, distribution of reads on genic elements, motif enrichment, relative position of reads of two datasets, differential gene counts, etc). To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains.
Performs the analysis of sequencing data from cross-linking, ligation and sequencing of hybrids (CLASH) experiments. hyb is able to recognize chimeric reads in other applications as well as for the analysis of UV cross-linking and analysis of cDNAs (CRAC), crosslinking and immunoprecipitation (CLIP), and RNA-Seq data. This tool can be useful and applicable to any next-generation sequencing datasets.
Analyzes PAR-CLIP data. PARpipe is a standalone software proposing a pipeline that consists of five main steps :(i) reads are prepared and aligned; (ii) interaction sites are defined; (iii) site-level metrics are generated; (iv) reads, cluster and groups are annotated and lastly; (v) the software performs binding sites relative to important transcript characteristics meta-analysis.
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Eduardo Eyras Group leader in Computational RNA Biology
Pompeu Fabra University