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  "Type": "Package",
  "Title": "A babysitter's package for reproducible RNA-seq analysis",
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  "Authors@R": "c(person(given = \"Shanwen\",\nfamily = \"Sun\",\nrole = c(\"cre\", \"aut\"),\nemail = \"sunshanwen@gmail.com\"),\nperson(given = \"Lei\",\nfamily = \"Xu\",\nrole = \"aut\"),\nperson(given = \"Quan\",\nfamily = \"Zou\",\nrole = \"aut\"))",
  "Description": "An automated pipe for reproducible RNA-seq analysis with\nthe minimal efforts from researchers. The package can process\nbulk RNA-seq data and single-cell RNA-seq data. You can only\nprovide the taxa name and the accession id of RNA-seq data\ndeposited in the National Center for Biotechnology Information\n(NCBI). After a cup of tea or longer, you will get formated\ngene expression data as gene count and transcript count based\non both alignment-based and alignment-free workflows.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
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  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev python3 libx11-dev",
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  "Date/Publication": "2026-04-28 12:44:47 UTC",
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  "Packaged": {
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    "User": "root"
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  "Author": "Shanwen Sun [cre, aut],\nLei Xu [aut],\nQuan Zou [aut]",
  "Maintainer": "Shanwen Sun <sunshanwen@gmail.com>",
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  "_created": "2026-10-04T17:12:59.000Z",
  "_published": "2026-10-07T14:20:41.780Z",
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    "warning": 2,
    "note": 14
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    "email": "sunshanwen@gmail.com",
    "login": "sunshanwen",
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  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
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  "_topics": [
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    "name": "Bioconductor",
    "followers": 470,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "extra/citation.html",
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    "extra/contents.json",
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    "align_free_quan",
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    "check_dep",
    "down_Ref",
    "down2quan",
    "fastq2quan",
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    "sra_download",
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      "page": "adapter_trim",
      "title": "Trim samples with adapter using cutadapt.",
      "topics": [
        "adapter_trim"
      ]
    },
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      "title": "alignment-based workflow",
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      "topics": [
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    },
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      "title": "Take averages with alignment-free and alignment-based quantification",
      "topics": [
        "average"
      ]
    },
    {
      "page": "check_dep",
      "title": "Check the existence of dependancies.",
      "topics": [
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      ]
    },
    {
      "page": "down_Ref",
      "title": "Download the latest reference genome, transcript and the corresponding annotation files from NCBI.",
      "topics": [
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      ]
    },
    {
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        "down2quan"
      ]
    },
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      ]
    },
    {
      "page": "qc_test",
      "title": "Quality assessments of raw sequence data.",
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      ]
    },
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      "topics": [
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      ]
    },
    {
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      "title": "scRNA expression quantification with Salmon.",
      "topics": [
        "scRNA_quan"
      ]
    },
    {
      "page": "sra_download",
      "title": "Download RNA-seq samples from the NCBI.",
      "topics": [
        "sra_download"
      ]
    },
    {
      "page": "sra2fastq",
      "title": "Convert SRA format to fastq format and return the sequencing type, i.e., single-end (SE) or paired-end (PE) reads.",
      "topics": [
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      ]
    }
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      "created": "2020-07-29 07:36:19",
      "modified": "2020-08-24 08:07:54",
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