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RNA Immunoprecipitation sequencing analysis bioinformatics software tools

RIP-Seq (or CLIP-Seq or PAR-CLIP) experiment shares many similarities to either full transcriptome sequencing (RNA-Seq)—since what is sequenced is a subset of the transcriptome itself—or sequencing applied to IP’ed chromatin (DNA…
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DFilter
Desktop

DFilter

A detection algorithm that identifies regulatory features in ChIP-seq,…

A detection algorithm that identifies regulatory features in ChIP-seq, DNase-seq and FAIRE-seq data more accurately than assay-specific algorithms. The mathematical formalism underlying DFilter…

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RIPSeeker
Desktop

RIPSeeker

Provides a comprehensive analytical suite for RIP-seq analysis, not only…

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…

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hiCLIP
Desktop

hiCLIP

Identifies RNA duplexes bound by a specific RNA-binding protein (RBP). hiCLIP…

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…

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Piranha
Desktop

Piranha

A peak-calling tool based on the zero-truncated negative binomial regression…

A peak-calling tool based on the zero-truncated negative binomial regression model that is able to incorporate external information to guide the site identification process. Piranha can also…

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ASPeak
Desktop

ASPeak

An abundance sensitive peak detection algorithm for RIP-Seq.

An abundance sensitive peak detection algorithm for RIP-Seq.

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TxCoords
Web
Server

TxCoords

Serves for transcriptomic peak re-mapping. TxCoords can help users to retrieve…

Serves for transcriptomic peak re-mapping. TxCoords can help users to retrieve the true sequences and to correct the incorrectly reported transcriptomic peaks. It also allows to visualize the…

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