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Reference genomes for alignment

Related links

Links to a selection of the software tools and databases used by this project are given below.

circRNA calling tools and databases

# Tools/Databases Description Version PubMed ID
1 CIRI2 An improved multithreading detection tool, CIRI2, that used an adapted maximum likelihood estimation based on multiple seed matching to identify back-spliced junction reads and to filter false positives derived from repetitive sequences and mapping errors v2.0.6 28334140
2 CIRCexplorer2 The successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. v2.3.8 27365365
3 DCC DCC is a python package intended to detect and quantify circRNAs with high specificity. v0.4.8 26556385
4 CIRI-full An accurate, high-throughput approach that uses both BSJ and reverse overlap (RO) features to reconstruct and quantify full-length circular RNAs from RNA-seq data sets. v2.0 30660194
5 RPFdb A public resource for hosting, analyzing and visualizing ribosome profiling (Ribo-seq) data. v2.0 30335166
6 REPIC A database dedicated to provide a new resource to investigate potential functiAons and mechanisms of N6-adenosine methylation (m6A) modifications. v1.0 32345346
7 IRESbase A database curated all experimentally validated IRESs in the published literature. v1.0 12457563
8 circBase A database for circular RNAs,hosting data from various Homo sapiens, Mus musculus, Caenorhabditis elegans, and Latimeria samples. v Jul. 2017 25234927
9 CIRCpedia An updated comprehensive database containing circRNA annotations from over 180 RNA-seq datasets across six different species. v2.0 30172046
10 circAtlas An integrated resource of circRNAs in vertebrates, integrating over one millions of circRNAs across 6 species (human, macaca, mouse, rat, pig, chicken) and a variety of tissues. v2.0 32345360
11 circBank A database of more than 14,000 human-annotated circRNAs, showing five features of the circRNA, including the miRNA binding site, conservation of circRNAs, m6A modification of circRNAs, mutation of circRNAs and protein-coding potential of circRNAs. v1.0 31023147
12 circRNADb A database containing 32,914 human exonic circRNAs carefully selected from diversified sources. v1.0 27725737
13 CSCD A database developed for cancer-specific circRNAs and their relationship with microRNAs and RNA-binding proteins. v1.0 29036403
14 exoRBase A repository of circular RNA (circRNA), long non-coding RNA (lncRNA) and messenger RNA (mRNA) derived from RNA-seq data analyses of human blood exosomes. v1.0 30053265
15 TSCD This database is constructed to provide a global view of tissue-specific circRNA in main tissues of human and mouse and is able to contribute to identify new markers for organogenesis and development disease. v1.0 27543790
16 Circ2Disease A database that manually curated experiment-supported human circRNAs, aims at providing a comprehesive associations between of circRNA and human diseases. v1.0 30030469