ALEXA-Seq statistics

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chevron_left Differential expression Alternative splicing events identification Known transcript quantification Differential usage Novel transcript quantification Normalization Alternative splicing visualization chevron_right
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Associated diseases

Associated diseases

ALEXA-Seq specifications


Unique identifier OMICS_01328
Name ALEXA-Seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some EnsEMBL gene models or mRNA and EST alignments.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for ALEXA-Seq

ALEXA-Seq in publications

PMCID: 5102823
PMID: 27157621
DOI: 10.1038/onc.2016.129

[…] important insight into targeting this key oncogenic driver., whole transcriptome shotgun sequencing (rnaseq) was completed on breast cancer cell lines and expression analysis was performed with the alexa-seq software package as previously described . briefly, this approach comprises (i) creation of a database of expression and alternative expression sequence ‘features’ (genes, transcripts, […]

PMCID: 4648566
PMID: 26609224
DOI: 10.4137/BBI.S28991

[…] alternative splicing events from rna-seq data. rmats is a statistical method for robust and flexible detection of genome-wide differential alternative splicing from paired or unpaired replicates. alexa-seq assesses the differential and alternative expression of the mrna isoforms after cataloging transcripts. an integrative analysis approach constructed an exon co-splicing network based […]

PMCID: 4556662
PMID: 26327458
DOI: 10.1371/journal.pone.0136653

[…] detect alternative splicing on the gene transcript level [, ]. katz et al. developed the miso model to infer estimates based on the reads that were mapped to sjs and alternative spliced exons []. alexa-seq is another method that was developed for alternative expression analysis of genetic features including exon regions, exon junctions, and intron regions []. other software tools designed […]

PMCID: 4482073
PMID: 25870410
DOI: 10.1093/nar/gkv311

[…] splicing., finally, we attempted to determine the extent of alternative splicing in individual samples. again, there were no existing programs that suited our needs. some programs, such as alexa-seq, splicetrap and spliceseq, are dependent on curated datasets specific to the human genome (–), while others, such as solas and miso, require transcript models to function (,). by creating […]

PMCID: 3890974
PMID: 24419370
DOI: 10.1038/srep03678

[…] in global transcript expression measurements., we next sought to determine the read duplicates in the sequencing libraries prepared by all the methods. we followed the approach adopted by alexa-seq where 1 million uniquely mapped reads (ncbi refseq mrna database) were randomly selected three times and the amount of read duplicates and the transcriptome coverage were assessed […]

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ALEXA-Seq institution(s)
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Department of Medicine, University of British Columbia, Vancouver, BC, Canada
ALEXA-Seq funding source(s)
Supported by the University of British Columbia, the Michael Smith Foundation for Health Research, the Natural Sciences and Engineering Research Council, Genome British Columbia, the Terry Fox Foundation, the Canadian Institutes of Health Research, the National Cancer Institute of Canada and the British Columbia Cancer Foundation.

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