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| build_index | Build index for mapping using Salmon |
| get_fastq | Download fastq files |
| get_metadata | Download metadata from GEO and SRA |
| get_srr | Download SRA run files |
| process_geo_rnaseq | A complete pipeline to process GEO RNA-seq data |
| run_fastqc | QC report for each fastq files using FastQC |
| run_multiqc | Generate combined QC report for Salmon and FastQC |
| run_salmon | Quantify transcript abundances using Salmon |
| run_tximport | Wrapper function to run tximport |
| trim_fastq | Trim fastq files using Trimmomatic |