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.

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

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