Man pages for jkruppa/viralDetectTools
Modules for a viral detection pipeline

aa_info_dbExample amino acid information db
aa_seqsAAStringSet of amino acid sequences
artificial_genome_mappingControl function for the artificial mapping
build_indexBuild a index for DNA and AA mapper
build_sample_infoInternal function to extract the sample information
check_hostExperimental function to check the host by blastn
collapse_dfCollapse a matrix by row
coverage_filterFilter the hits by the coverage
dna_seqsDNAStringSet of DNA sequences
empty_map_pep_listInternal empty object for pepe mapping
ete2_plotControl function for the ete3 phylogenetic trees
fastq_quality_controlMain fastq quality function
fastq_trimmerInternal trimmomatic call function
fq2faA wrapper for seqtk to convert fastq to fasta
generate_decoy_readsGenerates (decoy) reads from a sequence
generate_readGenerates a _single_ read from a sequence
get_bowtie2_cmdWrapper to build up the Bowtie2 command
get_consensus_dfGet the consenus sequence of the read hits to the reference
get_pauda_hitsInternal parse function for PAUDA
get_seq_chunks_by_thresholdDivide sequences into chunks
get_sub_filesGather the files for one sample run
infected_fastqExample fastq files
is.namedSmall tester if a object is named
map_dna_refDNA mapping function
map_pep_refAmino mapping function
mapping_dna_plotMapping the viral read hits to the reference
NHS_10001_consensusOutput of get_consensus_df
NHS_10001_count_tblOutput of ord_findings
NHS_10001_map_aa_listOutput of map_pep_ref
NHS_10001_map_dna_listOutput of map_dna_ref
ord_findingsOrder the hits of the mapping
plot_time_samplePlot the processed files in a dir
prepare_file_listGet all the files prepared in a directory
random_dna_seqShuffle a sequence with a kept kmer distribution
run_batch_jobFunction to run the pipeline on one folder
sam2bam_serialWrapper function for samtools
set_par_listS4 class of the parameter list
set_program_listPath to the external program executables
setup_aa_info_sample_sqliteFunction to build up the aa_info_sample_sqlite database
setup_aa_info_sqliteFunction to build up the aa_info_sqlite database
setup_species_info_sqliteFunction to build up the species_info_sqlite database
strain_info_dbExample species infro db
talkAdvanced message functionality by time stamp
tbl_sqlite_checkTest function to check the sqlite2 databases for consistency
TIMESmall wrapper to extract the time from Sys.time()
jkruppa/viralDetectTools documentation built on Jan. 22, 2018, 3:38 p.m.