SCENIC:cisTarget databases数据库下载

List of databases for the cisTarget family of tools (e.g. RcisTarget, SCENIC/pySCENIC, and cisTopic).

To choose the database appropiate for your analysis, start by selecting the species and ranking type (i.e. What do you want to analyze: genes or regions?).

Note that the download size is typically over 1GB (100GB for mammal region databases), we recommend downloading the files with zsync_curl (see the Help with downloads).

Related files:

  • sha256sum.txt: To confirm whether the file was succesfuly downloaded
  • TF annotation: Annotation to transcripton factors for the motifs or ChIP-seq tracks in each collection (30-100 Mb)
    • Human TFs (motif collection v8 / v9); (ChIP-seq v1 hg19 / hg38)
    • Mouse TFs (motif collection v8 / v9)
    • Fly TFs (motif collection v8 / v9); (ChIP-seq v1 dm6)

Column info:


  • Human (Homo sapiens)
  • Mouse (Mus musculus)
  • Fly (Drosophila melanogaster)

Ranking type:

  • Region: The ranking contains regions (i.e. for analyses of region-sets from ATAC-seq, ChIP-seq, …)
  • Genes: The ranking contains genes.

Distance: For gene rankings only. Indicates the search space around the TSS of gene in which the motif is scored:

  • 500bpUp: 500bp upstream of TSS
  • TSS+/-10kb: 10kb around the TSS (total: 20kb)
  • TSS+/-5kb: 5kb around the TSS (total: 10kb)
  • 5kbUp,FullTx: 5kb upstream TSS and transcript introns
  • 500bpUp100Dw: 500bp upstream of TSS, and 100bp downstream.

Motif or track collection:

  • Motifs – Version 8 (mc8nr): 20003 motifs
  • Motifs – Version 9 (mc9nr): 24453 motifs
  • TF ChIP-seq – Version 1 (tc_v1):
    • dm6: 1503 tracks
    • hg19: 3040 tracks
    • hg38: 2993 tracks

nOrt: Number of orthologous species used to select the regions based on conservation. In case of doubt of which version to use: 7 species is normally appropiate for most analyses.

Genome: Genome version used to construct the ranking. For region-based analyses it is important that this version matches your data! Gene annotation version is shown in parenthesis.

Database name: Database name (add the extensions to obtain specific file names, e.g. .feather or .feather.zsync).

Download URL: Link to the database (.feather file, and its size).

List of databases:


打赏 微信打赏,为服务器增加100M流量 微信打赏,为服务器增加100M流量 支付宝打赏,为服务器增加100M流量 支付宝打赏,为服务器增加100M流量
上一篇 2022年3月21日 下午12:55
下一篇 2022年4月1日 下午2:38


  • 序列比对


  • Python学习资源总结

    前言 知乎:路人甲 微博:玩数据的路人甲 微信公众号:一个程序员的日常   在知乎分享已经有一年多了,之前一直有朋友说我的回答能整理成书籍了,一直偷懒没做,最近有空仔细整…

  • 复旦大学学位与研究生教育国内期刊指导目录

    国内期刊指导目录 社会科学 学科 刊物名称 主办单位 级别 综合类 K1000001 中国社会科学 中国社会科学院 A类 K1000002 战略与管理 中国战略与管理研究会 A类 …

    网络资源 2022年2月26日
  • had non-zero exit status

    解决方案1:install.packages(‘*package_name’, dependencies = TRUE)

    Python 2020年11月7日
  • Pheatmap包使用

    Pheatmap简介: Pretty Heatmaps——Implementation of heatmaps that offers more control over dime…

    R 2020年3月15日