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Pipelines | CLIP-seq analysis

These software pipelines provide out-of-the box solutions for cross-linking immunoprecipitation sequencing analysis by combining a number of specific analysis programs together.

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pyCRAC
Desktop

pyCRAC

Permits the analysis of Nrd1-Nab3-RNA interactions. pyCRAC combines many…

Permits the analysis of Nrd1-Nab3-RNA interactions. pyCRAC combines many popular cross-linking and immunoprecipitation (CLIP)/ cross-linking and cDNA analysis (CRAC) analysis methods. It can be used…

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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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hiclipr
Desktop

hiclipr

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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PARCLIP_suite
Desktop

PARCLIP_suite PhotoActivatable-Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation

Allows to study RNA-RNA binding protein (RBP) interactions in human cell lines.…

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…

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CTK
Desktop

CTK CLIP Tool Kit

Provides a set of tools for flexible, streamlined, comprehensive cross-linking…

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…

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CLIPSeqTools
Desktop

CLIPSeqTools

A highly flexible computational suite that can perform analysis from raw…

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…

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Pyicos
Desktop

Pyicos

Analyses mapped reads from diverse High-throughput sequencing (HTS)…

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…

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miRTarCLIP
Desktop

miRTarCLIP

A systematic approach for mining miRNA-target sites from CLIP-Seq and PAR-CLIP…

A systematic approach for mining miRNA-target sites from CLIP-Seq and PAR-CLIP sequencing data, and integrated the workflow with a graphical web-based browser, which provides a user friendly…

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hyb
Desktop

hyb

Performs the analysis of sequencing data from cross-linking, ligation and…

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…

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