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RNA editing site detection software tools | RNA sequencing data analysis

RNA editing generates post-transcriptional sequence changes that can be deduced from RNA-seq data, but detection typically requires matched genomic sequence or multiple related expression data sets.Source text:(Zhang and Xiao 2015) Genome…
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LNCediting
Dataset

LNCediting Long Non Coding editing

A database of comprehensive information about Adenosine-to-Inosine editing…

A database of comprehensive information about Adenosine-to-Inosine editing sites in long non-coding RNAs (lncRNAs) across human, rhesus, mouse, and fly, to explore their potential functions.…

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GIREMI
Desktop

GIREMI Genome-independent Identification of RNA Editing by Mutual Information

A method that can identify RNA editing sites using one RNA-seq data set without…

A method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data. GIREMI calculates the mutual information (MI) of the mismatch pairs identified in the…

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RNAEditor
Desktop

RNAEditor

AnalyzeS RNA editing events from RNA sequencing data. RNAEditor maps the reads…

AnalyzeS RNA editing events from RNA sequencing data. RNAEditor maps the reads to the genome, calculates sequence variations, filters for “non-editing sites” and applies a cluster algorithm to…

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RDDpred
Desktop

RDDpred

A useful tool for investigating condition-specific RNA-editing with RNA-seq.…

A useful tool for investigating condition-specific RNA-editing with RNA-seq. RDDpred is a Random Forest RDD classifier. It reports potentially true RNA-editing events from RNA-seq data. RDDpred was…

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SPRINT
Desktop

SPRINT SNP-free RNA editing IdeNtification Toolkit

Identifies RNA editing sites (RESs) by clustering single nucleotide variant…

Identifies RNA editing sites (RESs) by clustering single nucleotide variant (SNV) duplets, bypassing the need of single nucleotide polymorphism (SNP) annotations. SPRINT is applicable to any RNA-seq…

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RES-Scanner
Desktop

RES-Scanner

Detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data…

Detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data from the same individuals or samples. To rigorously identify potential false positives resulting from genetic variants,…

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JACUSA
Desktop

JACUSA JAVA framework for accurate SNV assessment

Predicts single-nucleotide variant (SNV) positions from head-to-head…

Predicts single-nucleotide variant (SNV) positions from head-to-head comparisons of read stacks/pileups from Illumina sequencing. JACUSA is a versatile one-stop solution to detect SNV positions from…

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RED
Desktop

RED RNA Editing sites Detector

An effective software for the identification and visualization of RNA editing…

An effective software for the identification and visualization of RNA editing sites from next-generation sequencing data. RED is highly flexible, including a variety of filters and stringent…

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RCARE
Web

RCARE RNA-sequence Comparison and Annotation for RNA Editing

Searches, annotates, and visualizes RNA-editing sites using thousands of…

Searches, annotates, and visualizes RNA-editing sites using thousands of previously known editing sites. RCARE can be used for comparative analyses between multiple samples.

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The RNA…
Dataset

The RNA Editing ATLAS

The first human inosinome atlas comprising 3,041,422 Adenine to Inosine events…

The first human inosinome atlas comprising 3,041,422 Adenine to Inosine events identified in six tissues from three healthy individuals. Matched directional total-RNA-Seq and whole genome sequence…

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ExpEdit
Web

ExpEdit

A web application for assessing RNA editing in human at known or user-specified…

A web application for assessing RNA editing in human at known or user-specified sites supported by transcript data obtained by RNA-Seq experiments. The most relevant step of the ExpEdit workflow is…

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REDItools
Desktop

REDItools

A suite of python scripts to perform high-throughput investigation of RNA…

A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data.

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