Function reference • bears

All functions

check_md5(): Check file integrity with md5sum

create_dir_structure(): Create a standard directory for bears

create_sample_info(): Search the SRA database and create a data frame of sample metadata

download_from_ena(): Download FASTQ files from ENA's FTP

fastp_is_installed(): Check if fastp is installed

fastq_exists(): Check if FASTQ files were properly downloaded

featureCounts(): Count reads with featureCounts

featureCounts2se(): Create a SummarizedExperiment object from featureCounts output

get_url_ena(): Get URL for each file in the ENA's FTP repository

gff2bed(): Convert GFF file to BED

infer_strandedness(): Infer library strandedness

kallisto2se(): Create a SummarizedExperiment object from kallisto output

kallisto_index(): Index the transcriptome for kallisto

kallisto_is_installed(): Check if kallisto is installed

kallisto_quantify(): Quantify expression with kallisto

mapping_pass(): Keep only samples that passed minimum requirements in STAR alignment

mapping_qc: Summary statistics of STAR mapping QC

multiqc_is_installed(): Check if multiqc is installed

remove_rrna(): Remove rRNA sequences from .fastq files with SortMeRNA

rseqc_is_installed(): Check if RSeQC is installed

salmon2se(): Create a SummarizedExperiment object from salmon output

salmon_index(): Index the transcriptome for salmon

salmon_is_installed(): Check if salmon is installed

salmon_quantify(): Quantify expression with salmon

sample_info: Sample metadata

sortmerna_is_installed(): Check if SortMeRNA is installed

star_align(): Align reads to a reference genome using STAR

star_genome_index(): Index genome for STAR alignment

star_is_installed(): Check if STAR is installed

stringtie2se(): Create a SummarizedExperiment object from StringTie output

stringtie_assemble(): Assemble transcripts with StringTie

stringtie_is_installed(): Check if StringTie is installed

stringtie_quantify(): Quantify expression in TPM with StringTie

subread_is_installed(): Check if subread is installed

summary_stats_fastp(): Get read quality summary statistics from fastp

summary_stats_salmon(): Get salmon mapping rate for each BioSample

summary_stats_star(): Get mapping summary statistics from STAR

taco_is_installed(): Check if TACO is installed

taco_merge(): Merge assembled transcripts with TACO

translate_strandedness(): Translate library orientation terminology for each program

trim_reads(): Trim low-quality bases and adapters using fastp

tx2gene: Transcript to gene mapping