Files in jkruppa/viralDetectTools
Modules for a viral detection pipeline

.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
NAMESPACE
R/artificial_genome_mapping.R R/build_subset_index.R R/class.R R/consensus.R R/coverage_filter.R R/data.R R/empty_obj.R R/ete3.R R/generate_decoy_reads.R R/get_bowtie2_cmd.R R/get_pauda_hits.R R/map_dna_ref.R R/map_pep_ref.R R/mapping_dna_plot.R R/methods.R R/oop_functions.R R/random_dna_seq.R R/run_batch_job.R R/sam2bam.R R/sqlite.R R/trimming.R R/utility.R README.md
data/NGS-10001.xlsx
data/NGS-10001_R1.fastq.gz
data/NGS-10001_R2.fastq.gz
data/NGS-10001_consensus.RDS
data/NGS-10001_consensus_statistics.xlsx
data/NGS-10001_map_dna_list.RDS
data/NGS-10001_map_pep_list.RDS
data/NHS_10001_consensus.rda
data/NHS_10001_count_tbl.rda
data/NHS_10001_map_aa_list.rda
data/NHS_10001_map_dna_list.rda
data/aa_info_db.RDS
data/aa_info_db.rda
data/aa_morbi_example.fa
data/aa_seqs.rda
data/dna_morbi_example.fa
data/dna_seqs.rda
data/infected_fastq.rda
data/strain_info_db.RDS
data/strain_info_db.rda
doc/pauda_changes.md doc/setup_ncbi_databse.md
img/NGS-10001_00.png
img/NGS-10001_01.png
img/NGS-10001_02.png
img/NGS-10001_tree.png
img/NGS-10001_xlsx.png
man/NHS_10001_consensus.Rd man/NHS_10001_count_tbl.Rd man/NHS_10001_map_aa_list.Rd man/NHS_10001_map_dna_list.Rd man/TIME.Rd man/aa_info_db.Rd man/aa_seqs.Rd man/artificial_genome_mapping.Rd man/build_index.Rd man/build_sample_info.Rd man/check_host.Rd man/collapse_df.Rd man/coverage_filter.Rd man/dna_seqs.Rd man/empty_map_pep_list.Rd man/ete2_plot.Rd man/fastq_quality_control.Rd man/fastq_trimmer.Rd man/fq2fa.Rd man/generate_decoy_reads.Rd man/generate_read.Rd man/get_bowtie2_cmd.Rd man/get_consensus_df.Rd man/get_pauda_hits.Rd man/get_seq_chunks_by_threshold.Rd man/get_sub_files.Rd man/infected_fastq.Rd man/is.named.Rd man/map_dna_ref.Rd man/map_pep_ref.Rd man/mapping_dna_plot.Rd man/ord_findings.Rd man/plot_time_sample.Rd man/prepare_file_list.Rd man/random_dna_seq.Rd man/run_batch_job.Rd man/sam2bam_serial.Rd man/set_par_list.Rd man/set_program_list.Rd man/setup_aa_info_sample_sqlite.Rd man/setup_aa_info_sqlite.Rd man/setup_species_info_sqlite.Rd man/strain_info_db.Rd man/talk.Rd man/tbl_sqlite_check.Rd
viralDetectTools.Rproj
jkruppa/viralDetectTools documentation built on Jan. 22, 2018, 3:38 p.m.