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FcircSEC (version 1.0.0)

Full Length Circular RNA Sequence Extraction and Classification

Description

Extract full length circular RNA sequences and classify circular RNA using the output of circular RNA prediction tools, reference genome and the annotation file corresponding to the reference genome. This package uses the output of circular RNA prediction tools such as 'CIRI', 'CIRCExplorer' and the output of other state-of-the-art circular RNA prediction tools. Details about the circular RNA prediction procedure can be found in 'Yuan Gao, Jinfeng Wang and Fangqing Zhao' (2015) and 'Zhang XO, Wang HB, Zhang Y, Lu X, Chen LL and Yang L' (2014) .

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install.packages('FcircSEC')

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13

Version

1.0.0

License

GPL-2

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Maintainer

Md. Hossain

Last Published

January 31st, 2020

Functions in FcircSEC (1.0.0)

get.fasta

Generating sequences from the reference genome with specific intervals
chr1

chr1 of Reference genome
circClassification

circRNA classification using trancript information and the bed file from the circRNA prediction tools
transcript_data

Transcript data obtained from gene annotation file.
output_CIRI

Output obtained from circRNA prediction tool.
transcriptExtract

Extracting transcript information from the annotation file
circSeqExt

Generating full length circRNA sequences
circRNA_classt

circRNA classification data
circRNA_genomic_sequence

Genomic sequences of circRNAs.
refGenchr1

Gene annotation of chromosome 1 of human reference genome.
circRNA_classb

circRNA classification data