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chevron_left Novel transcript quantification Reference-based transcriptome assembly chevron_right
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iReckon specifications

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Unique identifier OMICS_01277
Name iReckon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for iReckon

iReckon in publications

 (5)
PMCID: 5547501
PMID: 28784092
DOI: 10.1186/s12864-017-4002-1

[…] focused on isoform quantification methods that aim to accurately quantify known transcripts. thus, those methods that focus on novel transcript discovery, such as stringtie [], slide [] and ireckon [], were excluded from this evaluation. after careful literature review, a total of seven tools were selected: cufflinks, rsem, tigar2, express, sailfish, kallisto and salmon. we used rsem […]

PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] transcripts, and replicates are essential to resolve false-positive calls (that is, mapping artifacts or contaminations) at the low end of signal detection. several methods, such as cufflinks [], ireckon [], slide [] and stringtie [], incorporate existing annotations by adding them to the possible list of isoforms. montebello [] couples isoform discovery and quantification using […]

PMCID: 4667643
PMID: 26522830
DOI: 10.1038/ncomms9718

[…] not fully successful at restoring optimal levels of correctly spliced transcripts., analysis of gene expression and minor intron retention using other rna-seq analysis methods (cufflinks, deseq and ireckon) led to similar findings (, and )., minor intron genes are overall enriched in functions and phenotypes relevant to roifman syndrome (for example, brain and skeletal phenotypes, cell cycle […]

PMCID: 4673975
PMID: 26338770
DOI: 10.1093/bioinformatics/btv488

[…] transcripts de novo from short read rna-seq data, of which cufflinks () is the most widely used. other methods are stringtie (), scripture (), trinity (), oases (velvet) (), soap-denovo-trans (), ireckon (), class (), flipflop (), isolasso (), mitie (), trans-abyss (), augustus (), traph ()., algorithms are classified by whether they use an alignment to a reference genome sequence, or whether […]

PMCID: 3851240
PMID: 24185837
DOI: 10.1038/nmeth.2714

[…] to benchmark methods to predict and quantify expressed transcripts from rna-seq data. results were evaluated from methods based on genome alignments (augustus, cufflinks, exonerate, gstruct, ireckon, mgene, mtim, nextgeneid, slide, transomics, trembly, tromer) as well as de novo assembly (oases and velvet). our results identify aspects of rna-seq analysis where current approaches […]


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iReckon institution(s)
Department of Computer Science, University of Toronto, ON, Canada

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