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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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Documentation


Maintainer


  • person_outline William Ritchie

Publication for IRFinder

IRFinder citations

 (6)
library_books

Widespread intronic polyadenylation diversifies immune cell transcriptomes

2018
Nat Commun
PMCID: 5928244
PMID: 29712909
DOI: 10.1038/s41467-018-04112-z

[…] 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 if […]

library_books

IntEREst: intron exon retention estimator

2018
BMC Bioinformatics
PMCID: 5896110
PMID: 29642843
DOI: 10.1186/s12859-018-2122-5

[…] tEREst results in conjunction with different statistical analysis packages implemented in IntEREst. Subsequently, we carried out comparison with both, the published results of the MDS analysis [] and IRfinder [], i.e. dedicated software for IR analysis. Note that all comparisons described in the following are based on the introns that were available in the both references used by the compared coun […]

library_books

Splicing of platelet resident pre mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications

2018
Sci Rep
PMCID: 5765118
PMID: 29323256
DOI: 10.1038/s41598-017-18985-5

[…] confirming 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 investigate […]

library_books

Intron retention enhances gene regulatory complexity in vertebrates

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

[…] atistics 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 of all […]

library_books

Intron retention is regulated by altered MeCP2 mediated splicing factor recruitment

2017
Nat Commun
PMCID: 5424149
PMID: 28480880
DOI: 10.1038/ncomms15134

[…] l (). 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 […]

library_books

Core genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats

2017
BMC Genomics
PMCID: 5372343
PMID: 28356070
DOI: 10.1186/s12864-017-3655-0

[…] m.nih.gov/genbank/). 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. […]

Citations

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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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