Tools

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CIRI [PubMed]

An efficient and unbiased algorithm for de novo circular RNA identification

URL: https://sourceforge.net/projects/ciri/files

CIRI2 [PubMed]

Circular RNA identification based on multiple seed matching

URL: https://sourceforge.net/projects/ciri/files/CIRI2

CIRI-AS [PubMed]

Comprehensive identification of internal structure and alternative splicing events in circular RNAs

URL: https://sourceforge.net/projects/ciri/files/CIRI-AS

CIRI-full [PubMed]

Reconstruction of full-length circular RNAs enables isoform-level quantification

URL: https://github.com/bioinfo-biols/CIRI-full

CIRI-vis [PubMed]

Visualization of circular RNAs and their internal splicing events from transcriptomic data

URL: https://github.com/bioinfo-biols/CIRI-vis

CIRIquant [PubMed]

Accurate quantification of circular RNAs identifies extensive circular isoform switching events

URL: https://github.com/bioinfo-biols/CIRIquant

CIRI-long [PubMed]

CIRI-long: circular RNA identifier using long-read sequencing data

URL: https://github.com/bioinfo-biols/CIRI-long

SEVtras [PubMed]

SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes

URL: https://github.com/bioinfo-biols/SEVtras

Flow2Spatial [PubMed]

The computational part of POTTLE (parallel flow projection and transfer learning-based spatial proteomics framework)

URL: https://github.com/bioinfo-biols/Flow2Spatial

NetMoss [PubMed]

Large-scale microbiome data integration enables robust biomarker identification

URL: https://github.com/xiaolw95/NetMoss2

MetaSort [PubMed]

MetaSort untangles metagenome assembly by reducing microbial community complexity

URL: https://sourceforge.net/projects/metasort

inGAP-CDG [PubMed]

A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes

URL: https://sourceforge.net/projects/ingap-cdg

inGAP-sf [PubMed]

The combination of direct and paired link graphs can boost repetitive genome assembly

URL: https://sourceforge.net/projects/ingap-sf

BreakSeek [PubMed]

a breakpoint-based algorithm for full spectral range INDEL detection

URL: https://sourceforge.net/projects/breakseek

RiboFR-Seq [PubMed]

a novel approach to linking 16S rRNA amplicon profiles to metagenomes

URL: https://sourceforge.net/projects/ribofr-seq