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

View on CRAN

Functions

arrange.jm Man page
best.layout Man page
big.peaks.col Man page
detect.ladder Man page
find.ladder Man page
Fragman Man page
get.scores Man page
homogenize.to.parentals Man page
homo.panel Man page
jm.conv Man page
ladder.corrector Man page
ladder.info.attach Man page
lapply_pb Man page
letter.to.jm Man page
my.plants Man page
num.to.lett Man page
overview Man page
overview2 Man page
pullup Man page
read.abif Man page
reals Man page
saturate Man page
score.easy Man page
separate Man page
storing.inds Man page
threshs Man page
transfft Man page
transp Man page

Files

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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