Files in USDA-ARS-GBRU/crossword
Breeding program similation sotware
DESCRIPTION
NAMESPACE
R/advance.R
R/combine_populations.R
R/count_chr_length.R
R/create_families.R
R/create_genome.R
R/create_haplotypes_from_scheme.R
R/create_marker_set.R
R/create_population.R
R/create_scheme.R
R/cross.R
R/dh.R
R/draw_PGplots.R
R/draw_haplotypes.R
R/draw_population.R
R/filter_parents.R
R/genomic_prediction.R
R/genotypes_out.R
R/get_genotypes.R
R/get_haplotype_matrix.R
R/get_level.R
R/get_marker_intersection.R
R/get_parental_genotypes.R
R/get_values.R
R/get_vr.R
R/haplotypes_in.R
R/haplotypes_out.R
R/mas.R
R/parental_contribution.R
R/phenotype.R
R/phenotype_out.R
R/physical2genomic.R
R/pick_individual.R
R/random_qtn_assign.R
R/run_batch.R
R/run_pipeline.R
R/select.R
R/select_haplotype.R
R/simulate_fastq.R
R/vcf2hapmap.R
README.md
inst/art/Darwin/454_profiles/GS_FLX_Titanium_profile/indel_error_profile
inst/art/Darwin/454_profiles/GS_FLX_Titanium_profile/length_dist
inst/art/Darwin/454_profiles/GS_FLX_Titanium_profile/qual_1st_profile
inst/art/Darwin/454_profiles/GS_FLX_Titanium_profile/qual_mc_profile
inst/art/Darwin/454_profiles/GS_FLX_profile/indel_error_profile
inst/art/Darwin/454_profiles/GS_FLX_profile/length_dist
inst/art/Darwin/454_profiles/GS_FLX_profile/qual_1st_profile
inst/art/Darwin/454_profiles/GS_FLX_profile/qual_mc_profile
inst/art/Darwin/ART_profiler_454/README
inst/art/Darwin/ART_profiler_454/art_profiler_454
inst/art/Darwin/ART_profiler_illumina/README
inst/art/Darwin/ART_profiler_illumina/art_profiler_illumina
inst/art/Darwin/ART_profiler_illumina/combinedAvg.pl
inst/art/Darwin/ART_profiler_illumina/empDist.pl
inst/art/Darwin/ART_profiler_illumina/fastqReadAvg.pl
inst/art/Darwin/ART_profiler_illumina/summation.pl
inst/art/Darwin/GPLv3.txt
inst/art/Darwin/Illumina_profiles/Emp100R1.txt
inst/art/Darwin/Illumina_profiles/Emp100R2.txt
inst/art/Darwin/Illumina_profiles/Emp36R1.txt
inst/art/Darwin/Illumina_profiles/Emp36R2.txt
inst/art/Darwin/Illumina_profiles/Emp44R1.txt
inst/art/Darwin/Illumina_profiles/Emp44R2.txt
inst/art/Darwin/Illumina_profiles/Emp50R1.txt
inst/art/Darwin/Illumina_profiles/Emp50R2.txt
inst/art/Darwin/Illumina_profiles/Emp75R1.txt
inst/art/Darwin/Illumina_profiles/Emp75R2.txt
inst/art/Darwin/Illumina_profiles/EmpMiSeq250R1.txt
inst/art/Darwin/Illumina_profiles/EmpMiSeq250R2.txt
inst/art/Darwin/Illumina_profiles/EmpR36R1.txt
inst/art/Darwin/Illumina_profiles/EmpR36R2.txt
inst/art/Darwin/Illumina_profiles/EmpR44R1.txt
inst/art/Darwin/Illumina_profiles/EmpR44R2.txt
inst/art/Darwin/Illumina_profiles/EmpR50R1.txt
inst/art/Darwin/Illumina_profiles/EmpR50R2.txt
inst/art/Darwin/Illumina_profiles/EmpR75R1.txt
inst/art/Darwin/Illumina_profiles/EmpR75R2.txt
inst/art/Darwin/Illumina_profiles/HiSeq2500L125R1.txt
inst/art/Darwin/Illumina_profiles/HiSeq2500L125R2.txt
inst/art/Darwin/Illumina_profiles/HiSeq2500L150R1.txt
inst/art/Darwin/Illumina_profiles/HiSeq2500L150R1filter.txt
inst/art/Darwin/Illumina_profiles/HiSeq2500L150R2.txt
inst/art/Darwin/Illumina_profiles/HiSeq2500L150R2filter.txt
inst/art/Darwin/Illumina_profiles/HiSeq2kL100R1.txt
inst/art/Darwin/Illumina_profiles/HiSeq2kL100R2.txt
inst/art/Darwin/Illumina_profiles/HiSeqXPCRfreeL150R1.txt
inst/art/Darwin/Illumina_profiles/HiSeqXPCRfreeL150R2.txt
inst/art/Darwin/Illumina_profiles/HiSeqXtruSeqL150R1.txt
inst/art/Darwin/Illumina_profiles/HiSeqXtruSeqL150R2.txt
inst/art/Darwin/Illumina_profiles/MiSeqv3L250R1.txt
inst/art/Darwin/Illumina_profiles/MiSeqv3L250R2.txt
inst/art/Darwin/Illumina_profiles/MiniSeqTruSeqL50.txt
inst/art/Darwin/Illumina_profiles/NextSeq500v2L75R1.txt
inst/art/Darwin/Illumina_profiles/NextSeq500v2L75R2.txt
inst/art/Darwin/SOLiD_profiles/getPsuedoProfile.pl
inst/art/Darwin/SOLiD_profiles/profile_default
inst/art/Darwin/SOLiD_profiles/profile_pseudo
inst/art/Darwin/aln2bed.pl
inst/art/Darwin/art_454
inst/art/Darwin/art_454_README.txt
inst/art/Darwin/art_SOLiD
inst/art/Darwin/art_SOLiD_README.txt
inst/art/Darwin/art_illumina
inst/art/Darwin/art_illumina_README.txt
inst/art/Darwin/examples/amplicon_reference.fa
inst/art/Darwin/examples/run_test_examples_454.sh
inst/art/Darwin/examples/run_test_examples_SOLiD.sh
inst/art/Darwin/examples/run_test_examples_illumina.sh
inst/art/Darwin/examples/testSeq.fa
inst/art/Darwin/map2bed.pl
inst/art/Linux/454_profiles/GS_FLX_Titanium_profile/indel_error_profile
inst/art/Linux/454_profiles/GS_FLX_Titanium_profile/length_dist
inst/art/Linux/454_profiles/GS_FLX_Titanium_profile/qual_1st_profile
inst/art/Linux/454_profiles/GS_FLX_Titanium_profile/qual_mc_profile
inst/art/Linux/454_profiles/GS_FLX_profile/indel_error_profile
inst/art/Linux/454_profiles/GS_FLX_profile/length_dist
inst/art/Linux/454_profiles/GS_FLX_profile/qual_1st_profile
inst/art/Linux/454_profiles/GS_FLX_profile/qual_mc_profile
inst/art/Linux/ART_profiler_454/README
inst/art/Linux/ART_profiler_454/art_profiler_454
inst/art/Linux/ART_profiler_illumina/README
inst/art/Linux/ART_profiler_illumina/art_profiler_illumina
inst/art/Linux/ART_profiler_illumina/combinedAvg.pl
inst/art/Linux/ART_profiler_illumina/empDist.pl
inst/art/Linux/ART_profiler_illumina/fastqReadAvg.pl
inst/art/Linux/ART_profiler_illumina/summation.pl
inst/art/Linux/GPLv3.txt
inst/art/Linux/Illumina_profiles/Emp100R1.txt
inst/art/Linux/Illumina_profiles/Emp100R2.txt
inst/art/Linux/Illumina_profiles/Emp36R1.txt
inst/art/Linux/Illumina_profiles/Emp36R2.txt
inst/art/Linux/Illumina_profiles/Emp44R1.txt
inst/art/Linux/Illumina_profiles/Emp44R2.txt
inst/art/Linux/Illumina_profiles/Emp50R1.txt
inst/art/Linux/Illumina_profiles/Emp50R2.txt
inst/art/Linux/Illumina_profiles/Emp75R1.txt
inst/art/Linux/Illumina_profiles/Emp75R2.txt
inst/art/Linux/Illumina_profiles/EmpMiSeq250R1.txt
inst/art/Linux/Illumina_profiles/EmpMiSeq250R2.txt
inst/art/Linux/Illumina_profiles/EmpR36R1.txt
inst/art/Linux/Illumina_profiles/EmpR36R2.txt
inst/art/Linux/Illumina_profiles/EmpR44R1.txt
inst/art/Linux/Illumina_profiles/EmpR44R2.txt
inst/art/Linux/Illumina_profiles/EmpR50R1.txt
inst/art/Linux/Illumina_profiles/EmpR50R2.txt
inst/art/Linux/Illumina_profiles/EmpR75R1.txt
inst/art/Linux/Illumina_profiles/EmpR75R2.txt
inst/art/Linux/Illumina_profiles/HiSeq2500L125R1.txt
inst/art/Linux/Illumina_profiles/HiSeq2500L125R2.txt
inst/art/Linux/Illumina_profiles/HiSeq2500L150R1.txt
inst/art/Linux/Illumina_profiles/HiSeq2500L150R1filter.txt
inst/art/Linux/Illumina_profiles/HiSeq2500L150R2.txt
inst/art/Linux/Illumina_profiles/HiSeq2500L150R2filter.txt
inst/art/Linux/Illumina_profiles/HiSeq2kL100R1.txt
inst/art/Linux/Illumina_profiles/HiSeq2kL100R2.txt
inst/art/Linux/Illumina_profiles/HiSeqXPCRfreeL150R1.txt
inst/art/Linux/Illumina_profiles/HiSeqXPCRfreeL150R2.txt
inst/art/Linux/Illumina_profiles/HiSeqXtruSeqL150R1.txt
inst/art/Linux/Illumina_profiles/HiSeqXtruSeqL150R2.txt
inst/art/Linux/Illumina_profiles/MiSeqv3L250R1.txt
inst/art/Linux/Illumina_profiles/MiSeqv3L250R2.txt
inst/art/Linux/Illumina_profiles/MiniSeqTruSeqL50.txt
inst/art/Linux/Illumina_profiles/NextSeq500v2L75R1.txt
inst/art/Linux/Illumina_profiles/NextSeq500v2L75R2.txt
inst/art/Linux/SOLiD_profiles/getPsuedoProfile.pl
inst/art/Linux/SOLiD_profiles/profile_default
inst/art/Linux/SOLiD_profiles/profile_pseudo
inst/art/Linux/aln2bed.pl
inst/art/Linux/art_454
inst/art/Linux/art_454_README.txt
inst/art/Linux/art_SOLiD
inst/art/Linux/art_SOLiD_README.txt
inst/art/Linux/art_illumina
inst/art/Linux/art_illumina_README.txt
inst/art/Linux/examples/amplicon_reference.fa
inst/art/Linux/examples/run_test_examples_454.sh
inst/art/Linux/examples/run_test_examples_SOLiD.sh
inst/art/Linux/examples/run_test_examples_illumina.sh
inst/art/Linux/examples/testSeq.fa
inst/art/Linux/map2bed.pl
inst/art/Windows/454_profiles/GS_FLX_Titanium_profile/null
inst/art/Windows/454_profiles/GS_FLX_profile/null
inst/art/Windows/ART_profiler_454/README
inst/art/Windows/ART_profiler_454/art_profiler_454
inst/art/Windows/ART_profiler_illumina/README
inst/art/Windows/ART_profiler_illumina/art_profiler_illumina
inst/art/Windows/ART_profiler_illumina/combinedAvg.pl
inst/art/Windows/ART_profiler_illumina/empDist.pl
inst/art/Windows/ART_profiler_illumina/fastqReadAvg.pl
inst/art/Windows/ART_profiler_illumina/summation.pl
inst/art/Windows/GPLv3.txt
inst/art/Windows/Illumina_profiles/Emp100R1.txt
inst/art/Windows/Illumina_profiles/Emp100R2.txt
inst/art/Windows/Illumina_profiles/Emp36R1.txt
inst/art/Windows/Illumina_profiles/Emp36R2.txt
inst/art/Windows/Illumina_profiles/Emp44R1.txt
inst/art/Windows/Illumina_profiles/Emp44R2.txt
inst/art/Windows/Illumina_profiles/Emp50R1.txt
inst/art/Windows/Illumina_profiles/Emp50R2.txt
inst/art/Windows/Illumina_profiles/Emp75R1.txt
inst/art/Windows/Illumina_profiles/Emp75R2.txt
inst/art/Windows/Illumina_profiles/EmpMiSeq250R1.txt
inst/art/Windows/Illumina_profiles/EmpMiSeq250R2.txt
inst/art/Windows/Illumina_profiles/EmpR36R1.txt
inst/art/Windows/Illumina_profiles/EmpR36R2.txt
inst/art/Windows/Illumina_profiles/EmpR44R1.txt
inst/art/Windows/Illumina_profiles/EmpR44R2.txt
inst/art/Windows/Illumina_profiles/EmpR50R1.txt
inst/art/Windows/Illumina_profiles/EmpR50R2.txt
inst/art/Windows/Illumina_profiles/EmpR75R1.txt
inst/art/Windows/Illumina_profiles/EmpR75R2.txt
inst/art/Windows/Illumina_profiles/HiSeq2500L125R1.txt
inst/art/Windows/Illumina_profiles/HiSeq2500L125R2.txt
inst/art/Windows/Illumina_profiles/HiSeq2500L150R1.txt
inst/art/Windows/Illumina_profiles/HiSeq2500L150R1filter.txt
inst/art/Windows/Illumina_profiles/HiSeq2500L150R2.txt
inst/art/Windows/Illumina_profiles/HiSeq2500L150R2filter.txt
inst/art/Windows/Illumina_profiles/HiSeq2kL100R1.txt
inst/art/Windows/Illumina_profiles/HiSeq2kL100R2.txt
inst/art/Windows/Illumina_profiles/HiSeqXPCRfreeL150R1.txt
inst/art/Windows/Illumina_profiles/HiSeqXPCRfreeL150R2.txt
inst/art/Windows/Illumina_profiles/HiSeqXtruSeqL150R1.txt
inst/art/Windows/Illumina_profiles/HiSeqXtruSeqL150R2.txt
inst/art/Windows/Illumina_profiles/MiSeqv3L250R1.txt
inst/art/Windows/Illumina_profiles/MiSeqv3L250R2.txt
inst/art/Windows/Illumina_profiles/MiniSeqTruSeqL50.txt
inst/art/Windows/Illumina_profiles/NextSeq500v2L75R1.txt
inst/art/Windows/Illumina_profiles/NextSeq500v2L75R2.txt
inst/art/Windows/SOLiD_profiles/getPsuedoProfile.pl
inst/art/Windows/SOLiD_profiles/profile_default
inst/art/Windows/SOLiD_profiles/profile_pseudo
inst/art/Windows/aln2bed.pl
inst/art/Windows/art_454.exe
inst/art/Windows/art_454_README.txt
inst/art/Windows/art_SOLiD.exe
inst/art/Windows/art_SOLiD_README.txt
inst/art/Windows/art_illumina.exe
inst/art/Windows/art_illumina_README.txt
inst/art/Windows/examples/amplicon_reference.fa
inst/art/Windows/examples/run_test_examples_454.sh
inst/art/Windows/examples/run_test_examples_SOLiD.sh
inst/art/Windows/examples/run_test_examples_illumina.sh
inst/art/Windows/examples/testSeq.fa
inst/art/Windows/map2bed.pl
inst/extdata/crossword.R
inst/extdata/crossword_output_01.zip
inst/extdata/crossword_output_01_test_mode.zip
inst/extdata/crossword_output_02_test_mode.zip
inst/extdata/crossword_script_input_file.script
inst/extdata/crossword_script_input_file.script_running_script.R
inst/extdata/crossword_script_input_file_gui.script
inst/extdata/crossword_script_input_file_test_mode_01.script
inst/extdata/crossword_script_input_file_test_mode_02.script
inst/extdata/gui_comments
inst/extdata/gui_input_output
inst/extdata/header_info
inst/extdata/listOfParameters
inst/extdata/peanut_input/chr_len.txt
inst/extdata/peanut_input/chr_siz.txt
inst/extdata/peanut_input/parental_genotypes.hapmap
inst/extdata/peanut_input/parental_genotypes.loc
inst/extdata/peanut_input/parental_genotypes_gen2phy_info
inst/extdata/peanut_input/peanut.gff
inst/extdata/peanut_input/peanut.vcf
inst/extdata/peanut_input/qtn_effects.efc
inst/extdata/peanut_input/select_genotypes.txt
inst/extdata/peanut_input/selected_parents_file
inst/extdata/test2.script
inst/icons/advance.gif
inst/icons/combine_populations.gif
inst/icons/convert.gif
inst/icons/count.gif
inst/icons/create_families.gif
inst/icons/create_genome.gif
inst/icons/create_populations.gif
inst/icons/cross.gif
inst/icons/dh.gif
inst/icons/draw.gif
inst/icons/edit_header.gif
inst/icons/filter.gif
inst/icons/genomic_prediction.gif
inst/icons/get.gif
inst/icons/in.gif
inst/icons/mas.gif
inst/icons/out.gif
inst/icons/reduce.gif
inst/icons/select.gif
inst/icons/simulate.gif
man/add_button.Rd
man/add_header_button.Rd
man/advance.Rd
man/combine_populations.Rd
man/count_chr_length.Rd
man/create_families.Rd
man/create_genome.Rd
man/create_haplotypes_from_scheme.Rd
man/create_marker_set.Rd
man/create_population.Rd
man/create_scheme.Rd
man/cross.Rd
man/crossword_gui.Rd
man/dh.Rd
man/draw_PGplots.Rd
man/draw_haplotypes.Rd
man/draw_population.Rd
man/filter_parents.Rd
man/genomic_prediction.Rd
man/genotypes_out.Rd
man/get_genotypes.Rd
man/get_haplotype_matrix.Rd
man/get_level.Rd
man/get_marker_intersection.Rd
man/get_parental_genotypes.Rd
man/get_values.Rd
man/get_vr.Rd
man/haplotypes_in.Rd
man/haplotypes_out.Rd
man/mas.Rd
man/parental_contribution.Rd
man/phenotype.Rd
man/phenotype_out.Rd
man/physical2genomic.Rd
man/pick_individual.Rd
man/random_qtn_assign.Rd
man/run_batch.Rd
man/run_pipeline.Rd
man/select.Rd
man/select_haplotype.Rd
man/simulate_fastq.Rd
man/vcf2hapmap.Rd
paper_simulations/Fig4_QTL-seq.zip
paper_simulations/Fig5A_FamSize_Generations.zip
paper_simulations/Fig5B_Genomic_selection.zip
paper_simulations/Fig6_allel_effect_polarity.zip
