├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── adapter_trim.R ├── align_based_quan.R ├── align_free_quan.R ├── average.R ├── check_dep.R ├── down2quan.R ├── down_Ref.R ├── fastq2quan.R ├── qc_test.R ├── quality_trim.R ├── scRNA_quan.R ├── sra2fastq.R └── sra_download.R ├── README.Rmd ├── README.md ├── cran-comments.md ├── inst ├── CITATION ├── News.md ├── extdata │ ├── Trimmed_test_read_2.fastq │ ├── test_Homo_sapiens.fna │ ├── test_Homo_sapiens.gff │ ├── test_gene_alignment_based_quantification.csv │ ├── test_gene_alignment_free_quantification.csv │ ├── test_read_1.fastq │ ├── test_read_2.fastq │ ├── test_read_2_fastqc.zip │ ├── test_transcript_Homo_sapiens.fna │ ├── test_transcript_alignment_based_quantification.csv │ └── test_transcript_alignment_free_quantification.csv └── prepDE_R.py ├── install_depends.sh ├── man ├── adapter_trim.Rd ├── align_based_quan.Rd ├── align_free_quan.Rd ├── average.Rd ├── check_dep.Rd ├── down2quan.Rd ├── down_Ref.Rd ├── fastq2quan.Rd ├── qc_test.Rd ├── quality_trim.Rd ├── scRNA_quan.Rd ├── sra2fastq.Rd └── sra_download.Rd ├── tests ├── testthat.R └── testthat │ ├── test-datasets_url.R │ ├── test-fastqc_r.R │ └── test-get_adapter.R └── vignettes ├── .gitignore └── vignette.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sunshanwen/BP4RNAseq/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sunshanwen/BP4RNAseq/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sunshanwen/BP4RNAseq/HEAD/DESCRIPTION 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