├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── build_index.R ├── get_fastq.R ├── get_metadata.R ├── get_srr.R ├── process_geo_rnaseq.R ├── run_fastqc.R ├── run_multiqc.R ├── run_salmon.R ├── run_tximport.R └── trim_fastq.R ├── README.md ├── inst ├── CITATION ├── extdata │ ├── NexteraPE-PE.fa │ ├── SRR5890521_pass.fastq │ ├── SRR5890521_transcripts_quant │ │ └── SRR5890521_quant_new.sf │ ├── TruSeq2-PE.fa │ ├── TruSeq2-SE.fa │ ├── TruSeq3-PE-2.fa │ ├── TruSeq3-PE.fa │ └── TruSeq3-SE.fa └── java │ └── trimmomatic-0.36.jar ├── java └── trimmomatic-0.36.jar ├── man ├── build_index.Rd ├── get_fastq.Rd ├── get_metadata.Rd ├── get_srr.Rd ├── process_geo_rnaseq.Rd ├── run_fastqc.Rd ├── run_multiqc.Rd ├── run_salmon.Rd ├── run_tximport.Rd └── trim_fastq.Rd └── vignettes ├── ref.bib └── vignette.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uc-bd2k/GREP2/HEAD/.Rbuildignore 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