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Citations per year

Number of citations per year for the bioinformatics software tool QAPA

Tool usage distribution map

This map represents all the scientific publications referring to QAPA per scientific context
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Associated diseases


Popular tool citations

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QAPA specifications


Unique identifier OMICS_28489
Alternative name Quantification of APA
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes




No version available


  • person_outline Quaid Morris
  • person_outline Benjamin Blencowe

Publication for Quantification of APA

QAPA citations


QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA seq data

Genome Biol
PMCID: 5874996
PMID: 29592814
DOI: 10.1186/s13059-018-1414-4
call_split See protocol

[…] QAPA quantifies APA levels using RNA-seq reads that uniquely map to 3′ UTR sequences demarcated by annotated poly(A) sites in last exons. The development and application of QAPA entailed establishing […]


Physician Awareness of Immune Responses to Polyethylene Glycol‐Drug Conjugates

PMCID: 5866984
PMID: 29383836
DOI: 10.1111/cts.12537

[…] sitivity of detection. The variance is possibly attributed to differences in the sensitivities of the APA‐detection assays used across studies. There currently lacks a standardized assay protocol for quantification of APA, a shortcoming that must be rectified for diagnosis of APA.At present, it is unclear why only a handful of PEGylated drugs appear to suffer from anti‐PEG antibody responses, whil […]


Eps15 membrane binding and bending activity acts redundantly with Fcho1 during clathrin mediated endocytosis

Mol Biol Cell
PMCID: 5007088
PMID: 27385343
DOI: 10.1091/mbc.E16-03-0151

[…] elegans were immobilized and 10 cortical Z-sections (0.2-μm steps) were acquired 23 min after oocyte ovulation in utero (Wang et al., 2014). Individual planes ∼1 μm from the eggshell were chosen for quantification of APA-2 puncta at the cortex. Only puncta that reached a minimal threshold of fluorescence intensity (after background subtraction) were used for quantification. To calculate the relat […]

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QAPA institution(s)
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Vector Institute, Toronto, ON, Canada
QAPA funding source(s)
Supported by an Ontario Graduate Scholarship and a CIHR Frederick Banting and Charles Best Canada Graduate Scholarship, and grants from CIHR (FDN-148434 and MOP125894) and Medicine by Design.

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