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
