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Fragman: an R package for fragment analysis

Overview of attention for article published in BMC Genomic Data, April 2016
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  • Above-average Attention Score compared to outputs of the same age (51st percentile)
  • Good Attention Score compared to outputs of the same age and source (76th percentile)

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Title
Fragman: an R package for fragment analysis
Published in
BMC Genomic Data, April 2016
DOI 10.1186/s12863-016-0365-6
Pubmed ID
Authors

Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa

Abstract

Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and quantitative trait loci (QTL) mapping, genetic diversity, pedigree analysis, and detection of heterozygosity. A handful of commercial and freely available software programs exist for fragment analysis; however, most of them are platform dependent and lack high-throughput applicability. We present the R package Fragman to serve as a freely available and platform independent resource for automatic scoring of DNA fragment lengths diversity panels and biparental populations. The program analyzes DNA fragment lengths generated in Applied Biosystems® (ABI) either manually or automatically by providing panels or bins. The package contains additional tools for converting the allele calls to GenAlEx, JoinMap® and OneMap software formats mainly used for genetic diversity and generating linkage maps in plant and animal populations. Easy plotting functions and multiplexing friendly capabilities are some of the strengths of this R package. Fragment analysis using a unique set of cranberry (Vaccinium macrocarpon) genotypes based on microsatellite markers is used to highlight the capabilities of Fragman. Fragman is a valuable new tool for genetic analysis. The package produces equivalent results to other popular software for fragment analysis while possessing unique advantages and the possibility of automation for high-throughput experiments by exploiting the power of R.

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X Demographics

The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 163 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Turkey 1 <1%
Germany 1 <1%
Unknown 161 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 38 23%
Student > Master 25 15%
Researcher 22 13%
Student > Bachelor 14 9%
Professor 11 7%
Other 30 18%
Unknown 23 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 77 47%
Biochemistry, Genetics and Molecular Biology 31 19%
Environmental Science 11 7%
Neuroscience 4 2%
Medicine and Dentistry 2 1%
Other 9 6%
Unknown 29 18%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 22 March 2023.
All research outputs
#14,600,874
of 25,374,917 outputs
Outputs from BMC Genomic Data
#429
of 1,204 outputs
Outputs of similar age
#149,486
of 313,608 outputs
Outputs of similar age from BMC Genomic Data
#5
of 21 outputs
Altmetric has tracked 25,374,917 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 1,204 research outputs from this source. They receive a mean Attention Score of 4.3. This one has gotten more attention than average, scoring higher than 63% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 313,608 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 51% of its contemporaries.
We're also able to compare this research output to 21 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 76% of its contemporaries.