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Peak calling software tools | CLIP-seq data analysis

Assessing peaks is a central step of the analysis to determine specific signal over the noise background for the identification of real binding sites. The number of identified peaks increases with the sequencing depth because weaker sites become…
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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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PARalyzer
Desktop

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.

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PIPE-CLIP
Web

PIPE-CLIP

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

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.

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iCLIPpro
Desktop

iCLIPpro

Permits to control systematic mis-assignments in individual-nucleotide…

Permits to control systematic mis-assignments in individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) data. iCLIPro first visualizes coinciding and noncoinciding fragment…

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CLIPper
Desktop

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…

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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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SARNAclust
Desktop

SARNAclust

Identifies RNA motifs at full structural resolution while also being able to…

Identifies RNA motifs at full structural resolution while also being able to simultaneously deconvolve multiple motifs. SARNAclust is a clustering algorithm for CLIP peaks that typically uses the…

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PARA-suite
Desktop

PARA-suite PAR-CLIP analyzer 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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omniCLIP
Desktop

omniCLIP

Identifies target sites via an unsupervised segmentation of the transcriptome.…

Identifies target sites via an unsupervised segmentation of the transcriptome. omniCLIP is a Bayesian method to detects regulatory regions from all of the aforementioned protocols. This method learns…

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PureCLIP
Desktop

PureCLIP

Allows to precisely capture protein-RNA interaction footprints from…

Allows to precisely capture protein-RNA interaction footprints from iCLIP/eCLIP-seq data. PureCLIP provides a promising method to analyse datasets, also for proteins with lower binding affinities or…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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TEToolkit
Desktop

TEToolkit

A method and software package for including both gene- and TE-associated…

A method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. TEtranscripts shows improved recovery of TE transcripts over…

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Pyicoclip
Desktop

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).…

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PAR-CLIP HMM
Desktop

PAR-CLIP HMM

A model-based approach to detect RNA-RBP binding sites in PAR-CLIP. PAR-CLIP…

A model-based approach to detect RNA-RBP binding sites in PAR-CLIP. PAR-CLIP HMM integrates models to identify enriched regions and high-confidence binding sites into one rigorous statistical model.…

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CLIP-PyL
Desktop

CLIP-PyL

Detects peaks in HITS-CLIP data and generates base-specific coverage metrics.…

Detects peaks in HITS-CLIP data and generates base-specific coverage metrics. CLIP-PyL needs aligned BAM files as input files along with a BED file containing the gene or transcript in which the user…

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HITS-CLIP…
Desktop

HITS-CLIP Analysis

Detects RNA-protein binding sites in HITS-CLIP. HITS-CLIP Analysis is a…

Detects RNA-protein binding sites in HITS-CLIP. HITS-CLIP Analysis is a model-based approach that provides essential MATLAB functions to implement a model for the identification of binding sites…

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MiClip
Desktop

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…

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