Cross-linking followed by IP sequencing bioinformatics software tools

CLIP-seq analysis steps

High-throughput sequencing of short RNA fragments directly associated with RNA-binding proteins enables transcriptome-wide mapping of protein binding sites on RNAs. Such binding sites can be enriched by either immunopurification of RNA–protein complexes (RIP) (Zhao et al.,…

Cross-linking followed by IP sequencing bioinformatics software tools

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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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wavClusteR
Desktop

wavClusteR

A statistical and computational framework for PAR-CLIP data analysis. A…

A statistical and computational framework for PAR-CLIP data analysis. A sensitive transition-centered algorithm specifically designed to resolve protein binding sites at high resolution in PAR-CLIP…

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GraphProt
Desktop

GraphProt

It can be used for modeling binding preferences of RNA-binding proteins from…

It can be used for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.

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deepnet-rbp
Desktop

deepnet-rbp

A deep learning framework to model the binding preferences of RNA-binding…

A deep learning framework to model the binding preferences of RNA-binding proteins (RBPs) by integrating the primary sequence, predicted secondary and tertiary structural profiles of the target…

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RNAcontext
Desktop
Web

RNAcontext

A motif finding method ideally suited for using large-scale RNA-binding…

A motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures.

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PARA-suite
Desktop

PARA-suite

A toolkit for processing and aligning short and error-prone sequencing reads.…

A toolkit for processing and aligning short and error-prone sequencing reads. PARA-suite is implemented in Java using HTSjdk, a Java API for high-throughput sequencing data formats. The PARA-suite…

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BMix
Desktop

BMix

A toolbox for analysing PAR-CLIP data and detecting T-to-C substitutions…

A toolbox for analysing PAR-CLIP data and detecting T-to-C substitutions induced following RNA-protein cross-linking. BMix uses a constrained three-component binomial mixture to account for the…

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CapR
Desktop

CapR

Calculates the probability that each RNA base position is located within each…

Calculates the probability that each RNA base position is located within each secondary structural context. Six contexts of RNA secondary structures were taken into account, according to the…

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ProbRNA
Desktop

ProbRNA

Methods for statistically modeling these structure-probing data and extracting…

Methods for statistically modeling these structure-probing data and extracting structural features from them.

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BackCLIP
Desktop

BackCLIP

Identifies the presence of common RNA background in a PAR-CLIP dataset. We used…

Identifies the presence of common RNA background in a PAR-CLIP dataset. We used the measured sets of non-specific RNA backgrounds to build a common background set. Each element from the common…

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DRME
Desktop

DRME Differential RNA MEthylation

A software package for the differential RNA methylation analysis at small…

A software package for the differential RNA methylation analysis at small sample size scenario from MeRIP-Seq data. The proposed model can effectively describe within-group biological variability at…

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DeBooster
Desktop

DeBooster Deep Boost

A framework to predict the sequence specificities of RNA-binding proteins from…

A framework to predict the sequence specificities of RNA-binding proteins from high-throughput CLIP-seq data. DeBooster provides an effective index to identify pathogenic mutations from normal…

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ssHMM
Desktop

ssHMM Sequence-structure hidden Markov model

Identifies de novo sequence-structure motifs in a set of RNA sequences bound by…

Identifies de novo sequence-structure motifs in a set of RNA sequences bound by a certain RNA-binding proteins (RBP). ssHMM combines a hidden Markov model (HMM) with Gibbs sampling to learn the joint…

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MatrixREDUCE
Desktop

MatrixREDUCE

Discovers the position-specific affinity matrices for unknown RNAbinding…

Discovers the position-specific affinity matrices for unknown RNAbinding factors and infers their condition-specific activities. MatrixREDUCE uses genome-wide occupancy data for a transcription…

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PAR-CLIP HMM
Desktop

PAR-CLIP HMM

Provides an integrative model to establish a joint distribution of read and…

Provides an integrative model to establish a joint distribution of read and mutation counts.

Curators for CLIP-seq analysis

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