Files in abshah/RADseqR
.DS_Store
.Rbuildignore
._.DS_Store
._.RData
._.Rbuildignore
._.Rhistory
._.Rproj.user
._.git
._.gitignore
._DESCRIPTION
._NAMESPACE
._R
._RADseqR.Rproj
._man
.gitignore
DESCRIPTION
NAMESPACE
R/._Calc_number_of_genotypes_per_sample_from_SNPtable.R
R/._add_ReadGroups_with_picard.R
R/._batch_1_whitelist.tsv
R/._call_SNPs_with_GATK.R
R/._convert_table_to_SNPtable.R
R/._create_RADseqR_project.R
R/._create_sequence_dict_with_picard.R
R/._execute_denovomap_from_stacks.R
R/._execute_process_radtags.R
R/._execute_sort_read_pairs_from_stacks.R
R/._execute_velvet_script_from_stacks.R
R/._fastx_artifacts_filter.R
R/._fastx_clipper.R
R/._fastx_fastq_to_fasta.R
R/._fastx_quality_stats.R
R/._fastx_renamer.R
R/._fastx_reverse_complement.R
R/._fastx_trimmer.R
R/._get_whitelist.R
R/._is_this_application_installed.R
R/._make_psuedoparent.R
R/._map_with_BWA_mem.R
R/._map_with_bowtie2.R
R/._map_with_bwa_and_remove_PCR_duplicates.R
R/._process_ddradtags_from_stacks.R
R/._read_VCF_table_and_apply_PNAS_2014_filters.R
R/Calc_number_of_genotypes_per_sample_from_SNPtable.R
R/add_ReadGroups_with_picard.R
R/apply_stacks_genotypes_filter.R
R/call_SNPs_with_GATK.R
R/call_SNPs_with_GATK_haplotyper.R
R/convert_table_to_SNPtable.R
R/create_RADseqR_project.R
R/create_sequence_dict_with_picard.R
R/execute_denovomap_for_populations.R
R/execute_denovomap_from_stacks.R
R/execute_process_radtags.R
R/execute_sort_read_pairs_from_stacks.R
R/execute_velvet_script_from_stacks.R
R/fastx_artifacts_filter.R
R/fastx_clipper.R
R/fastx_fastq_to_fasta.R
R/fastx_quality_stats.R
R/fastx_renamer.R
R/fastx_reverse_complement.R
R/fastx_trimmer.R
R/get_whitelist.R
R/is_this_application_installed.R
R/make_psuedoparent.R
R/map_with_BWA_mem.R
R/map_with_bowtie2.R
R/map_with_bwa_and_remove_PCR_duplicates.R
R/merge_sam_files.R
R/parse_DM_log_file.R
R/parse_PR_log_file.R
R/process_ddradtags_from_stacks.R
R/read_VCF_table_and_apply_PNAS_2014_filters.R
R/remove_pcr_duplicates.R
RADseqR.Rproj
man/._add_ReadGroups_with_picard.Rd
man/._call_SNPs_with_GATK.Rd
man/._create_RADseqR_project.Rd
man/._create_sequence_dict_with_picard.Rd
man/._execute_denovomap_from_stacks.Rd
man/._execute_sort_read_pairs_from_stacks.Rd
man/._execute_velvet_script_from_stacks.Rd
man/._fastq_to_fasta.Rd
man/._fastx_artifacts_filter.Rd
man/._fastx_clipper.Rd
man/._fastx_quality_stats.Rd
man/._fastx_renamer.Rd
man/._fastx_reverse_complement.Rd
man/._fastx_trimmer.Rd
man/._get_whitelist_from_haplotype_list.Rd
man/._hello.Rd
man/._is_the_application_installed.Rd
man/._make_psuedoparent.Rd
man/._map_with_bowtie2.Rd
man/._map_with_bwa_and_remove_PCR_duplicates.Rd
man/._map_with_bwa_mem.Rd
man/._process_ddradtags_from_stacks.Rd
man/._process_radtags_from_stacks.Rd
man/add_ReadGroups_with_picard.Rd
man/call_SNPs_with_GATK.Rd
man/create_RADseqR_project.Rd
man/create_sequence_dict_with_picard.Rd
man/execute_denovomap_from_stacks.Rd
man/execute_sort_read_pairs_from_stacks.Rd
man/execute_velvet_script_from_stacks.Rd
man/fastq_to_fasta.Rd
man/fastx_artifacts_filter.Rd
man/fastx_clipper.Rd
man/fastx_quality_stats.Rd
man/fastx_renamer.Rd
man/fastx_reverse_complement.Rd
man/fastx_trimmer.Rd
man/get_whitelist_from_haplotype_list.Rd
man/hello.Rd
man/is_the_application_installed.Rd
man/make_psuedoparent.Rd
man/map_with_bowtie2.Rd
man/map_with_bwa_and_remove_PCR_duplicates.Rd
man/map_with_bwa_mem.Rd
man/process_ddradtags_from_stacks.Rd
man/process_radtags_from_stacks.Rd
