GitHub link
Documentation

Project management and pipeline frameworks

· Pypiper - Easy pipelines (python).

· Looper - Run your pipelines across lots of samples (python).

· projectInit - A project initialization manager (R).

· RefGenie - A scripted reference genome index folder organizer for pipelines (python).

· pepkit - A description of standard PEP format for annotating project metadata.

· pep - A python package for interfacing with PEPs.

· pep - An R package for interfacing with PEPs (alpha).

Pipelines

· dnameth_pipelines - Pipelines for Whole Genome and Reduced Representation Bisulfite Sequencing.

· rnapipe - Pipeline for RNA-seq data.

Data analysis software

· pararead - Parallel processing of sequence reads (python).

· MIRA - Methylation-based Inference of Regulatory Activity. Bioconductor package for DNA methylation data

· LOLA - Genomic Locus Overlap Analysis (R). Enrichment of genomic ranges.

· 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