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Bioinformatics and Genomic Medicine (Yang Lab)

Softwares

CIRCexplorer1

A combined strategy to identify junction reads from back spliced exons and intron lariats.

CIRCexplorer2

CIRCexplorer2 is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization.

CIRCpseudo

CIRCpseudo is a pipeline to map back-splicing junction sequences for circRNA-derived pseudogenes detection. Using this pipeline, you could previously detect circRNA-derived pseudogenes in genome, after maual check you could do further characterizations for them.

CIRCfinder

CIRCfinder is a pipeline to map junction reads for circular intronic RNAs (ciRNAs). Using this pipeline, you could determine the exact boundaries of interested ciRNAs, so that you could do further characterizations for them.

TERate

TERate is a computational pipeline to measure transcription elongation rates (TERs) with 4sUDRB-Seq.

CLEAR/CIRCexplorer3

CLEAR is a computational pipeline for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq.

bsRNA-seq-m5C

bsRNA-seq-m5C is a pipeline for m5C calling.

CSI

CSI is a pipeline to quantitate RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns.

CIRCshapemapper

CIRCshapemapper is a pipeline to analyze circSHAPE-MaP for circRNA secondary structure prediction.

RADAR

RADAR is a pipeline to detect and visualize all possible twelve-types of RNA editing events from RNA-seq datasets.

CDCscreen

CDCscreen is a computational pipeline for Cas13d-mediated circRNA screen to identify functional circular RNAs.

BEIDOU

BEIDOU is a Unified toolkit to identify base editor or prime editor induced DNA off-target sites.

CFBI

CFBI is the custom Perl and Shell scripts for calculating frequencies of base substitutions and indels.

SCAPTURE

SCAPRUTE is a deep learning-embedded pipeline that captures polyadenylation information from 3 prime tag-based RNA-seq of single cells.

Databases

CIRCpedia

CIRCpedia is an integrative database, aiming to annotating alternative back-splicing and alternative splicing in circRNAs across different cell lines.

CIRCpedia v2

CIRCpedia v2 is an updated circRNA database with integrated information of circRNA annotation, expression, and conservation.

BEable-GPS

BEable-GPS is a database to profile the accessibility of BEs for targeting pathogenic SNVs and provide gRNA designs for pathogenic SNVs and genomic targets.


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