Fragman: Fragment Analysis in R

Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).

AuthorGiovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Date of publication2016-09-01 19:36:53
MaintainerGiovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
LicenseGPL-3
Version1.0.7
http://www.wisc.edu

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Files in this package

Fragman
Fragman/inst
Fragman/inst/CITATION
Fragman/NAMESPACE
Fragman/data
Fragman/data/datalist
Fragman/data/my.plants.RData
Fragman/R
Fragman/R/homogenize.to.parentals.R Fragman/R/overview.R Fragman/R/lapply_pb.R Fragman/R/letter.to.jm.R Fragman/R/threshs.R Fragman/R/ladder.info.attach.R Fragman/R/Fragma-internal.R Fragman/R/homo.panel.R Fragman/R/ladder.corrector.R Fragman/R/reals.R Fragman/R/pullup.R Fragman/R/get.scores.R Fragman/R/detect.ladder.R Fragman/R/best.layout.R Fragman/R/jm.conv.R Fragman/R/big.peaks.col.R Fragman/R/saturate.R Fragman/R/transfft.R Fragman/R/read.abif.R Fragman/R/transp.R Fragman/R/num.to.lett.R Fragman/R/storing.inds.R Fragman/R/arrange.jm.R Fragman/R/score.easy.R Fragman/R/overview2.R Fragman/R/separate.R Fragman/R/find.ladder.R
Fragman/MD5
Fragman/DESCRIPTION
Fragman/man
Fragman/man/reals.Rd Fragman/man/arrange.jm.Rd Fragman/man/transfft.Rd Fragman/man/overview.Rd Fragman/man/homogenize.to.parentals.Rd Fragman/man/Fragman-package.Rd Fragman/man/saturate.Rd Fragman/man/num.to.lett.Rd Fragman/man/lapply_pb.Rd Fragman/man/separate.Rd Fragman/man/best.layout.Rd Fragman/man/ladder.info.attach.Rd Fragman/man/big.peaks.col.Rd Fragman/man/transp.Rd Fragman/man/read.abif.Rd Fragman/man/jm.conv.Rd Fragman/man/score.easy.Rd Fragman/man/pullup.Rd Fragman/man/detect.ladder.Rd Fragman/man/ladder.corrector.Rd Fragman/man/threshs.Rd Fragman/man/overview2.Rd Fragman/man/my.plants.Rd Fragman/man/get.scores.Rd Fragman/man/storing.inds.Rd Fragman/man/homo.panel.Rd Fragman/man/find.ladder.Rd Fragman/man/letter.to.jm.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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