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RIP-seq/CLIP-seq software tools

Sequencing software tools

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., 2010) or cross-linking followed by IP (CLIP) (Darnell et al., 2010). Although peak identification in ChIP-Seq data has been extensively explored, there are few bioinformatics tools tailored for peak calling on analogous datasets for RNA-binding proteins.

ASPeak

OMIC_00566

ASPeak

An abundance sensitive peak detection algorithm for RIP-Seq.

An abundance sensitive peak detection algorithm for RIP-Seq.

BackCLIP

OMIC_09507

BackCLIP

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

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 background set has a score that reflects its presence in…

BMix

OMIC_09854

BMix

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

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 different sources of noise in PAR-CLIP data and…

CapR

OMIC_09337

CapR

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

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 well-established Turner energy model of RNAs. These…

CLIPSeqTools

OMIC_10669

CLIPSeqTools

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

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…

CLIPZ

OMIC_02256

CLIPZ

Environment to analyse binding sites of RNA-binding proteins.

Environment to analyse binding sites of RNA-binding proteins.

dCLIP

OMIC_05261

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.

deepnet-rbp

OMIC_10246

deepnet-rbp

A deep learning framework to model the binding preferences of RNA-binding proteins (RBPs)…

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 sites. Our framework considered RNA tertiary structure…

DFilter

OMIC_08442

DFilter

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

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 facilitates integrative analysis of data from virtually…

GraphProt

OMIC_02252

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.

HITS-CLIP Analysis

OMIC_05265

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.

mCarts

OMIC_00567

mCarts

A hidden Markov model (HMM)-based methods to predict clusters RNA motif sites.

A hidden Markov model (HMM)-based methods to predict clusters RNA motif sites.

MiClip

OMIC_06672

MiClip

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

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 subsequent validation experiments. The MiClip algorithm…

MicroMUMMIE

OMIC_00401

MicroMUMMIE

A specific model, implemented within the MUMMIE framework, for predicting micro-RNA…

A specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data.

miRTarCLIP

OMIC_05260

miRTarCLIP

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

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 interface and detailed annotations of MTIs.

MIRZA

OMIC_05259

MIRZA

A tool for predicting miRNA-target site interactions.

A tool for predicting miRNA-target site interactions.

PAR-CLIP data analyzer

OMIC_02137

PAR-CLIP data analyzer
PARalyzer

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

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

PAR-CLIP HMM

OMIC_05266

PAR-CLIP HMM

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

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

PARma

OMIC_05258

PARma

A complete data analysis software for AGO-PAR-CLIP experiments to identify target sites…

A complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites.

PIPE-CLIP

OMIC_02254

PIPE-CLIP

A web tool which provides a pipeline for both bioinformaticians and biologist to identify…

A web tool which provides a pipeline for both bioinformaticians and biologist to identify the most likely cross-linking sites from PAR-CLIP, HITS-CLIP and iCLIP sequencing data.

Piranha

OMIC_00568

Piranha

A peak-caller for CLIP- and RIP-Seq data.

A peak-caller for CLIP- and RIP-Seq data.

ProbRNA

OMIC_02195

ProbRNA

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

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

Pyicoclip

OMIC_08898

Pyicoclip

An implementation of the modified false discovery rate algorithm proposed in (Yeo et al.,…

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). Pyicoclip is typically used in CLIP-Seq data and…

RBPmotif

OMIC_03826

RBPmotif

Implements tools to identify binding preferences of RNA-binding proteins (RBPs).

Implements tools to identify binding preferences of RNA-binding proteins (RBPs).

RIPSeeker

OMIC_00569

RIPSeeker

A statistical package for identifying protein-associated transcripts from RIP-seq…

A statistical package for identifying protein-associated transcripts from RIP-seq experiments.

RNAcontext

OMIC_02253

RNAcontext

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

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.

RNAmotifs

OMIC_02287

RNAmotifs

A method that evaluates the sequence around differentially regulated alternative exons to…

A method that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs.

wavClusteR

OMIC_02255

wavClusteR

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

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 data was developed. This method employes a Bayesian…

Zagros

OMIC_07049

Zagros

A motif discovery software for CLIP-Seq high-throughput protein-RNA interaction data.…

A motif discovery software for CLIP-Seq high-throughput protein-RNA interaction data. Given the regions of significant enrichment for reads Zagros can characterize the binding site for the given RBP. Zagros contains two additional programs to…