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gsrc (version 1.1)

Genome Structure Rearrangement Calling in Genomes with High Synteny

Description

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.

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Install

install.packages('gsrc')

Monthly Downloads

44

Version

1.1

License

GPL-3

Issues

0

Pull Requests

0

Stars

1

Forks

2

Maintainer

Fabian Grandke

Last Published

October 17th, 2016

Functions in gsrc (1.1)

check_raw

Check raw data
filt_snps

Filter SNPs
intens_theta

Preprocess raw values and calculate Intensity and Theta values
call_geno

Genotype with kmeans using three clusters
cnv

Copy Number Variation
geno_baf_rratio

Genotype with kmeans using three clusters
find_blocks

Find Synteny Blocks
filter_cnv

Filter Copy number variations
find_peak

Find peaks
remove_suffix

Remove suffix from sample names
plot_cnv

Plot Copy Number Variations
plot_trans_locations

Plot translocations
plot_gsr

Plot all chromosomes of a sample
plot_global

Plot all chromosomes of a population
interpol

Interpolate cluster means
plot_raw_snp

Plot raw SNP
read_sample_sheets

Read sample sheet(s)
plot_samp

Plot all chromosomes of a sample
read_intensities

Read multiple idat files.
rename_samples

Rename sample names
synteny_info

Class for synteny information
trans_location

Find translocations
segm

Segmentation of R ratio values
split_sb

Split synteny blocks
require_package

Require package wrapper
filt_samp

Filter Samples