Project management and pipeline software

  • Pypiper - Easy pipelines (python).
  • Looper - Run your pipelines across lots of samples (python).
  • project.init - A project initialization manager (R).
  • RefGenie - A scripted reference genome index folder organizer for pipelines (python).

Data analysis software

  • pararead - Parallel processing of sequence reads (python).
  • MIRA - Methylation-based Inference of Regulatory Activity (R).
  • LOLA - Genomic Locus Overlap Analysis (R).
  • simpleCache - Fast caching (R).
  • dipPeak - A peak caller for DNase data (R).

Web resources and services

Raw Data

  • GSE88826 - DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma
  • GSE65196 - Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics
  • GSE54908 - Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection’

Training and skills resources

Paper Year Accession
DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma 2017 GSE88826
Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics 2015 GSE65196
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection 2013 GSE54908