Man pages for uashogeschoolutrecht/structural_colours
Package For Project Structural Colour
| add_accession_contigs_megahit_dir | Function to concatenate megahit final contigs into one fasta... |
| blast | This function is a wrapper for the blast+ suite tools. |
| cat_rename_seq_id | Concatenate binned contigs into one file per sample and add... |
| fastqc_multisummary | Plots sum stats of multiple fastqc results |
| gbtools_plot | Gbtools bin plot for Shiny |
| get_data_ebi | This function downloads metadata and fastq files from ebi by... |
| get_fastq | This function uses the fastq_ftp col from the filereport to... |
| get_filereport | This function downloads the filereport of a study and saves... |
| get_metadata | This functions uses the MGnify API to connect to ebi to... |
| grinder | Runs the biogrinder program to create artificial fastq reads... |
| makeblastdb | Run makeblastdb and create output folder in data |
| run_bbmap | Function to run bbmap program from r |
| run_CAT | This function runs CAT on input contigs and creates the... |
| run_fastqc | Function to run fastqc program on the supplied file |
| run_megahit | This script is a R wrapper for the bash script megahit.sh to... |
| run_metabat2 | This function runs the metabat2 program script |
| run_prokka | Script to activate and run prokka on metagenome |
| run_sc_pipeline | Shotgun metagenomic analysis and marker gene detection... |
| run_trimmomatic | This function uses trimmomatic to trim input fastq files and... |
