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| add.diag | Add something to the diagonal |
| alpha_to_beta | Moore-Penrose-Transfomration |
| analyze.bv | Analyze genomic values |
| analyze.population | Analyze allele frequency of a single marker |
| bit.snps | Decoding of bitwise-storing in R |
| bit.storing | Bitwise-storing in R |
| breeding.diploid | Breeding function |
| breeding.intern | Internal function to simulate one meiosis |
| bv.development | Devolopment of genetic/breeding value |
| bv.development.box | Devolopment of genetic/breeding value |
| bv.standardization | BV standardization |
| calculate.bv | Calculate breeding values |
| cattle_chip | Cattle chip |
| chicken_chip | chicken chip |
| clean.up | Clean-up recombination points |
| codeOriginsR | Origins-coding(R) |
| compute.costs | Compute costs of a breeding program |
| compute.costs.cohorts | Compute costs of a breeding program |
| compute.snps | Compute genotype/haplotype |
| compute.snps_single | Compute genotype/haplotype in gene editing application |
| creating.diploid | Generation of the starting population |
| creating.phenotypic.transform | Calculate breeding values |
| creating.trait | Generation of genomic traits |
| decodeOriginsR | Origins-Decoding(R) |
| derive.loop.elements | Derive loop elements |
| edges.fromto | gen/database/cohorts conversion |
| edit_animal | Internal gene editing function |
| effect.estimate.add | Estimation of marker effects |
| ensembl.map | Ensemble Map |
| epi | Martini-Test function |
| ex_json | ex_json |
| ex_pop | ex_pop |
| find.chromo | Position detection |
| find.snpbefore | Position detection |
| generation.individual | Function to generate a new individual |
| get.age.point | Derive age point |
| get.bv | Export underlying true breeding values |
| get.bve | Export estimated breeding values |
| get.class | Derive class |
| get.cohorts | Export Cohort-names |
| get.creating.type | Derive creating type |
| get.cullingtime | Derive time of culling |
| get.database | gen/database/cohorts conversion |
| get.death.point | Derive death point |
| get.geno | Derive genotypes of selected individuals |
| get.genotyped | Derive genotyping status |
| get.haplo | Derive haplotypes of selected individuals |
| get.id | Derive class |
| get.individual.loc | Export location of individuals from the population list |
| get.infos | Extract bv/pheno/geno of selected individuals |
| get.map | Map generation |
| get.pca | Derive class |
| get.pedigree | Derive pedigree |
| get.pedigree2 | Derive pedigree including grandparents |
| get.pedigree3 | Derive pedigree parents and grandparents |
| get.pedmap | Generate plink-file (pedmap) |
| get.pheno | Export underlying phenotypes |
| get.pheno.off | Export underlying phenotypes |
| get.pheno.off.count | Export underlying phenotypes |
| get.recombi | Derive genetic origins |
| get.reliabilities | Export underlying reliabilities |
| get.selectionindex | Export underlying selection index |
| get.time.point | Derive time point |
| get.vcf | Generate vcf-file |
| insert.bve | Export estimated breeding values |
| json.simulation | Generation of the starting population |
| kinship.development | Devolopment of genetic/breeding value |
| kinship.emp | Empirical kinship |
| kinship.emp.fast | Empirical kinship |
| kinship.exp.store | Derive expected kinship |
| ld.decay | Generate LD plot |
| maize_chip | maize chip |
| miesenberger.index | Miesenberger Index |
| mutation.intro | Mutation intro |
| new.base.generation | Set new base generation |
| OGC | Optimal genetic contribution |
| pedmap.to.phasedbeaglevcf | Perform imputing/phasing |
| pig_chip | pig chip |
| sheep_chip | sheep chip |
| sortd | Apply sort and unique |
| ssGBLUP | Single Step GBLUP |
| summary.population | Summary Population |
| vlist | Derive class |