Bioinformatics and Interdisciplinary Technologies (BITs), 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.
