gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

Pipeline to read and analyze raw SNP array data. The data is preprocessed and normalized. Genotypes and CNVs are called. Synteny blocks are calculated and translocations detected. The results can be plotted with special functions.

Install the latest version of this package by entering the following in R:
install.packages("gsrc")
AuthorFabian Grandke [cre, aut], Birgit Samans [aut]
Date of publication2016-10-17 12:41:19
MaintainerFabian Grandke <grafabian@gmail.com>
LicenseGPL-3
Version1.1
http://github.com/grafab/gsrc

View on CRAN

Functions

call_geno Man page
check_raw Man page
cnv Man page
filter_cnv Man page
filt_samp Man page
filt_snps Man page
filt_snps.norm_data Man page
filt_snps.raw_data Man page
find_blocks Man page
find_peak Man page
geno_baf_rratio Man page
intens_theta Man page
interpol Man page
plot_cnv Man page
plot_global Man page
plot_gsr Man page
plot_raw_snp Man page
plot_samp Man page
plot_trans_locations Man page
read_intensities Man page
read_sample_sheets Man page
remove_suffix Man page
rename_samples Man page
rename_samples.norm_data Man page
rename_samples.raw_data Man page
require_package Man page
segm Man page
split_sb Man page
synteny_info Man page
trans_location Man page

Files

inst
inst/CITATION
inst/doc
inst/doc/synteny.R inst/doc/introduction.R
inst/doc/synteny.html
inst/doc/introduction.html
inst/doc/introduction.Rmd
inst/doc/synteny.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test_segm.R tests/testthat/test_filt_samp.R tests/testthat/test_cnv.R tests/testthat/read_intensities.R tests/testthat/test_check_raw.R tests/testthat/test_geno_rratio_baf.R tests/testthat/test_filt_snps.R tests/testthat/test_intens_theta.R
NAMESPACE
NEWS
R
R/synteny.R R/preprocess.R R/plot.R R/raw.R R/filter.R R/tools.R R/process.R
vignettes
vignettes/brassica_synteny_filtered.rda
vignettes/introduction_files
vignettes/introduction_files/figure-html
vignettes/introduction_files/figure-html/unnamed-chunk-22-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-20-3.png
vignettes/introduction_files/figure-html/unnamed-chunk-17-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-32-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-14-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-28-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-12-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-29-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-31-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-21-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-23-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-17-2.png
vignettes/introduction_files/figure-html/unnamed-chunk-18-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-30-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-33-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-20-2.png
vignettes/introduction_files/figure-html/unnamed-chunk-25-1.png
vignettes/introduction_files/figure-html/unnamed-chunk-20-1.png
vignettes/cotton_synteny_filtered.rda
vignettes/introduction_cache
vignettes/introduction_cache/html
vignettes/introduction_cache/html/unnamed-chunk-31_7d400f8476971a879c0ec0e5feb79517.rdx
vignettes/introduction_cache/html/unnamed-chunk-31_7d400f8476971a879c0ec0e5feb79517.RData
vignettes/introduction_cache/html/unnamed-chunk-31_7d400f8476971a879c0ec0e5feb79517.rdb
vignettes/introduction_cache/html/__packages
vignettes/introduction.Rmd
vignettes/synteny.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/read_sample_sheets.Rd man/check_raw.Rd man/filt_snps.Rd man/plot_global.Rd man/plot_gsr.Rd man/find_peak.Rd man/filter_cnv.Rd man/read_intensities.Rd man/require_package.Rd man/geno_baf_rratio.Rd man/call_geno.Rd man/remove_suffix.Rd man/trans_location.Rd man/plot_cnv.Rd man/synteny_info.Rd man/segm.Rd man/interpol.Rd man/plot_samp.Rd man/plot_trans_locations.Rd man/plot_raw_snp.Rd man/split_sb.Rd man/cnv.Rd man/rename_samples.Rd man/find_blocks.Rd man/filt_samp.Rd man/intens_theta.Rd

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.