IRFinder protocols

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IRFinder specifications

Information


Unique identifier OMICS_16786
Name IRFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Perl, Shell (Bash)
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline William Ritchie <>

Publication for IRFinder

IRFinder in pipelines

 (2)
2018
PMCID: 5765118
PMID: 29323256
DOI: 10.1038/s41598-017-18985-5

[…] using star version 2.5.0a. differentially expressed transcripts (fold-change ≥ |1.5|, fdr ≤ 0.05) were identified as described., intron retention level (ir ratio) was computed for each sample using irfinder tool with standard parameters. irfinder excludes features that overlap with introns such as microrna or snornas as these may confound the accurate measurement of true intron levels., ir […]

2017
PMCID: 5688624
PMID: 29141666
DOI: 10.1186/s13059-017-1339-3

[…] for each sample are provided in additional file : table s5 and figure s22. gene body coverage was determined using the genebody coverage module from the rseqc package (v2.6.3) []., we used the irfinder algorithm [] for the detection of ir events in all known introns. irfinder estimates the abundance of ir by computing the ratio between gene transcripts retaining an intron and the sum […]


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IRFinder in publications

 (6)
PMCID: 5928244
PMID: 29712909
DOI: 10.1038/s41467-018-04112-z

[…] (n = 64) and group b-filtered (n = 100). the r survival package was used to perform the kaplan–meier analysis for the two groups., retained introns were identified using a modified version of the irfinder algorithm. to avoid genes with a complex genomic architecture, we removed genes that overlap with other genes in either the sense of antisense strand. an intron was categorized as retained […]

PMCID: 5765118
PMID: 29323256
DOI: 10.1038/s41598-017-18985-5

[…] the possible presence of an active spliceosome in platelets (table ). interesting, several pre-mrnas were also found. indeed, analyzing rna-seq data obtained under the same conditions with irfinder, we detected a total of 5628 statistically significant intron retention (ir) events, 3014 of which detected with high confidence in at least two of the three biological replicates […]

PMCID: 5688624
PMID: 29141666
DOI: 10.1186/s13059-017-1339-3

[…] differentiation in human and mouse []. to study the functional conservation of ir events in species spanning 430 million years, we identified ir in terminally differentiated granulocytes using the irfinder algorithm [] (see “”). for every intron the algorithm computes the ir ratio (in the range of 0–1), which is an approximation of the proportion of total transcripts that retained the given […]

PMCID: 5424149
PMID: 28480880
DOI: 10.1038/ncomms15134

[…] (). our previous conservative algorithm to detect ir identified 121 introns from 86 transcripts that show differential ir in granulocytes compared to promyelocytes. we have now refined our previous irfinder algorithm to better estimate ir from sequencing reads and to include more introns in our analysis. this is achieved mainly by removing biases such as low mappability and overlapping features […]

PMCID: 5372343
PMID: 28356070
DOI: 10.1186/s12864-017-3655-0

[…] the accession numbers of the genomes are listed in additional file : table s1 and s2. source codes and examples for our methods are available at https://github.com/danwangjessica/irfinder., dw collected the datasets, designed and developed the pipelines, performed and analysed the experiments, and wrote the paper. sl and fg provided conceptual and technical guidance […]


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IRFinder institution(s)
Bioinformatics Laboratory, Centenary Institute, Camperdown, Australia; Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA; Boston & Harvard Medical School, Boston, MA, USA; Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, Australia; CNRS, Montpellier, France; Pompeu Fabra University, UPF, Barcelona, Spain; Sydney Medical School, University of Sydney, Sydney, NSW, Australia; Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, Australia; Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS, Paris, France; Catalan Institution for Research and Advanced Studies, ICREA, Barcelona, Spain; Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
IRFinder funding source(s)
This work was supported by the Agence Nationale de la Recherche (ANR 143683), the National Health and Medical Research Council (grant #1061906, #1080530, #1128175, #1126306), grants BIO2014-52566-R from the MINECO (Spanish Government) and FEDER funds, by AGAUR (2014-SGR1121), and by the Sandra Ibarra Foundation for Cancer (FSI2013).

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