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

Desktop app
G T A T C G C T A Piranha Piranha

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…

G T A T C G C T A CLIPper CLIPper

CLIPper

Defines peaks in CLIP-seq dataset. CLIPper combines features from many CLIP…

Defines peaks in CLIP-seq dataset. CLIPper combines features from many CLIP peak-finding algorithms. To reduce false-positives, it employes a three-pass filter on our peaks. For each gene it…

Desktop app
G T A T C G C T A PARA-suite PARA-suite

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…

Desktop app
G T A T C G C T A Deep Boost Deep Boost

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…

Desktop app
G T A T C G C T A MatrixREDUCE MatrixREDUCE

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…

Desktop app
G T A T C G C T A Sequence-structure… Sequence-structure hidden Markov model

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…

Desktop app
G T A T C G C T A Differential RNA… Differential RNA MEthylation

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…

Desktop app
G T A T C G C T A deepnet-rbp deepnet-rbp

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…

Desktop app
G T A T C G C T A BMix BMix

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…

Desktop app
G T A T C G C T A BackCLIP BackCLIP

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…

Desktop app
G T A T C G C T A CapR CapR

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…

Desktop app
G T A T C G C T A Pyicoclip Pyicoclip

Pyicoclip

An implementation of the modified false discovery rate algorithm proposed in…

An implementation of the modified false discovery rate algorithm proposed in (Yeo et al., 2009) to determine which clusters are significant in a list of genomic regions (like genes or transcripts).…

Desktop app
G T A T C G C T A DFilter DFilter

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…

Desktop app
G T A T C G C T A PAR-CLIP HMM PAR-CLIP HMM

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.

Desktop app
G T A T C G C T A dCLIP dCLIP

dCLIP

An easy-to-use command line tool for quantitative CLIP-seq comparative analysis.

An easy-to-use command line tool for quantitative CLIP-seq comparative analysis.

Desktop app
G T A T C G C T A HITS-CLIP Analysis HITS-CLIP Analysis

HITS-CLIP Analysis

A model-based approach to detect RNA-protein binding sites in HITS-CLIP.

A model-based approach to detect RNA-protein binding sites in HITS-CLIP.

Desktop app
G T A T C G C T A wavClusteR wavClusteR

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…

Desktop app
G T A T C G C T A GraphProt GraphProt

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.

Desktop app
Web app
G T A T C G C T A RNAcontext RNAcontext

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.

Desktop app
G T A T C G C T A ProbRNA ProbRNA

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.

Desktop app
G T A T C G C T A PAR-CLIP data analyzer PAR-CLIP data analyzer

PARalyzer PAR-CLIP data analyzer

Tool to generate a high resolution map of interaction sites between RNA-binding…

Tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.

Desktop app
G T A T C G C T A MiClip MiClip

MiClip

A model-based approach to identify high-confidence protein-RNA binding sites…

A model-based approach to identify high-confidence protein-RNA binding sites from CLIP-seq datasets. This approach assigns a probability score for each potential binding site to help prioritize…

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.