Corset statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Corset
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Tool usage distribution map

This map represents all the scientific publications referring to Corset per scientific context
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Protocols

Corset specifications

Information


Unique identifier OMICS_12944
Name Corset
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Version 1.07
Stability Stable
Requirements
SAMtools
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Alicia Oshlack

Additional information


https://github.com/Oshlack/Corset/wiki

Publication for Corset

Corset citations

 (23)
call_split

Transcriptome analysis of pecan seeds at different developing stages and identification of key genes involved in lipid metabolism

2018
PLoS One
PMCID: 5919011
PMID: 29694395
DOI: 10.1371/journal.pone.0195913
call_split See protocol

[…] ty (version 2.0.6) with default parameters [, ]. The paired-end reads from each library were mapped to de novo assemblies using bowtie (version 1.1.1) []. The transcript abundance was estimated using Corset (version 1.03) []. The count data generated from Corset were processed using the edgeR package []. Transcripts with less than one count per million reads (CPM) for at least three libraries were […]

library_books

The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen–encoding var genes

2018
PLoS Biol
PMCID: 5864071
PMID: 29529020
DOI: 10.1371/journal.pbio.2004328

[…] ost abundant domain clusters up-regulated in severe malaria in this analysis (). DBLε3 was also up-regulated in every analysis we performed () and was part of DC11 in the separate assembly transcript Corset analysis, although the DC11 transcripts were all different from the up-regulated DBLε3 transcripts from the individual domain analysis. A cluster similar to DBLεpam5 from the pregnancy malaria- […]

library_books

Functional Characterization and Signaling Systems of Corazonin and Red Pigment Concentrating Hormone in the Green Shore Crab, Carcinus maenas

2018
Front Neurosci
PMCID: 5775280
PMID: 29379412
DOI: 10.3389/fnins.2017.00752

[…] tomes for neural and Y-organ tissues, and a third comprising YO and epidermis tissues, were assembled separately. Differential gene expression analysis between YO and epidermis tissues was done using Corset (Davidson and Oshlack, ) and edgeR (Robinson et al., ) to identify GPCRs upregulated in the YO relative to the epidermis. Transcriptomes were mined for contigs putatively encoding neuropeptide […]

library_books

Transcriptome Analysis in Haematococcus pluvialis: Astaxanthin Induction by High Light with Acetate and Fe2+

2018
Int J Mol Sci
PMCID: 5796124
PMID: 29316673
DOI: 10.3390/ijms19010175

[…] comb transcripts that corresponded to paralogous genes through simplifying each component’s de Bruijn graph. After these three steps, the assembled results of TRINITY.fasta were finally obtained.Then Corset was used to hierarchically cluster transcripts by expression patterns and the number of reads which had been blasted to transcripts []. After hierarchical clustering by Corset, the longest Clus […]

library_books

Origin and evolution of the nuclear auxin response system

2018
eLife
PMCID: 5873896
PMID: 29580381
DOI: 10.7554/eLife.33399.035

[…] was used to map individual sample to the respective transcriptome assemblies using default parameters. Further, to improve the read count estimation and reduce the redundancy in Trinity transcripts, Corset () was implemented to estimate raw read counts using the Bowtie2 mapped alignment data. The obtained raw read counts were normalized and differentially expressed genes (Padj <0.01) were identif […]

library_books

A dual transcript discovery approach to improve the delimitation of gene features from RNA seq data in the chicken model

2017
PMCID: 5827264
PMID: 29183907
DOI: 10.1242/bio.028498

[…] EST), can be used to create consensus gene sequences. However, since both programs perform their clustering based on all transcript sequences, paralogous genes may be erroneously merged. In contrast, Corset () identifies sequence similarity between transcripts by identifying multi-mapped reads resulting from re-mapping of reads against the reconstructed transcriptome. Although this program accurat […]


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Corset institution(s)
Murdoch Childrens Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia; Department of Genetics, University of Melbourne, Melbourne, VIC, Australia
Corset funding source(s)
Supported by an NHMRC Career Development Fellowship APP1051481.

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