• I Get RNA-seq data!
  • 1 Data
    • 1.1 Human
    • 1.2 Mouse
    • 1.3 Study explorer
    • 1.4 How to cite recount3
  • 2 Quick Access
    • 2.1 Quick recount3
    • 2.2 Quick snapcount
    • 2.3 Quick raw files
  • 3 How to ask for help
    • 3.1 Gitter
    • 3.2 Bioconductor Support website
    • 3.3 GitHub Issues
  • II Details
  • 4 Quality check fields
  • 5 Bioconductor
    • 5.1 recount3
    • 5.2 snapcount
      • 5.2.1 Basic queries
    • 5.3 megadepth
  • 6 Raw Files
    • 6.1 Data source vs collection
    • 6.2 Annotation files
    • 6.3 Project-level count files
    • 6.4 Project-level metadata files
    • 6.5 Sample-level BigWig files
  • 7 Related software
    • 7.1 Beyond recount3
  • 8 Related analyses
    • 8.1 Beyond recount3
  • III Expand ReCount
  • 9 Your data
    • 9.1 Process your data
    • 9.2 Contribute your collections
      • 9.2.1 Collection metadata
      • 9.2.2 Collection project location
  • 10 Join the ReCount team!
  • R session information
  • References

recount3: human and mouse public RNA-seq data

8 Related analyses

The code for the analyses shown in the recount3 paper is available through the following GitHub repositories.

  • Re-analyses of Intropolis, ASCOT, FANTOM-CAT, and Zhang et al’s data: https://github.com/ChristopherWilks/monorail_paper
  • Human gene-level analyses: https://github.com/hansenlab/recount3_human_gene
  • Mouse gene-level analyses: https://github.com/hansenlab/recount3_mouse_gene

8.1 Beyond recount3

Some analyses beyond recount3 are available through the following locations:

  • runs: https://github.com/nellore/runs for processing the data behind Intropolis and recount2 with Rail-RNA
  • fcr2: https://github.com/eddieimada/fcr2, with https://github.com/LieberInstitute/marchionni_projects as a companion repository
  • recount-analyses: https://github.com/leekgroup/recount-analyses for recount2
  • intropolis: https://github.com/nellore/intropolis
  • phenopredict: https://github.com/leekgroup/phenopredict, https://github.com/ShanEllis/phenopredict_phenotypes and https://github.com/ShanEllis/phenopredict_usecase
  • recount-brain: https://github.com/LieberInstitute/recount-brain which is an example collection
  • insp: https://github.com/LieberInstitute/insp which is an example use case of recount.bwtool
  • recountNNLS: https://github.com/JMF47/recountNNLS
  • recount_pandey: https://github.com/LieberInstitute/recount_pandey which involved modifying code from recount-website/recount-prep