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

Files in this package

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.

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