Softwares & Databases
Softwares & Databases
Please see the Xiao-Ou Zhang Lab's GitHub page for our latest software packages.
APApedia database →
DatabaseAPApedia is a comprehensive database of alternative cleavage and polyadenylation (APA) events in development. It catalogs APA events across a wide range of developmental contexts in human and mouse. (Wang et al., Advanced Science, 2025)
TE-TSS database →
DatabaseTE-TSS is a database of transposon (TE)-derived transcription start sites (TSSs). It collects TE-derived TSSs in human and mouse, and lets users search, browse and download them together with their usage across biosamples. (Gu et al., Nucleic Acids Research, 2024)
RAMPAGE analysis toolkit →
SoftwareThe RAMPAGE analysis toolkit is a standardized pipeline for quality control, data cleaning, peak calling and peak annotation of RAMPAGE data. We used it to identify Pol III-transcribed Alu elements (Zhang et al., Genome Research, 2019), alternative TSSs (Moore et al., Genome Research, 2022), expressed snRNA variants (Zhang et al., Genome Research, 2026) and transposon-derived TSSs (Zhang et al., Nature Communications, 2026).
Developed during the PI's Ph.D. and postdoctoral fellowship.
CIRCpseudo →
SoftwareCIRCpseudo maps back-splicing junction sequences to identify pseudogenes derived from circular RNAs, revealing how circRNAs can be written back into the genome. (Dong et al., Cell Research, 2016)
CIRCexplorer/CIRCexplorer2 →
SoftwareCIRCexplorer is a comprehensive toolkit for circRNA analysis. It supports multiple aligners for circular RNA reads, enables de novo assembly of novel circRNA transcripts, and facilitates the characterization of alternative (back-)splicing events. (Zhang et al., Cell, 2014) (Zhang et al., Genome Research, 2016)
CIRCfinder →
SoftwareCIRCfinder maps junction reads to identify circular intronic RNAs (ciRNAs) and to pinpoint their exact boundaries. (Zhang et al., Molecular Cell, 2013)
