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.
· peppy - A python package for interfacing with PEPs.
· pepr - An R package for interfacing with PEPs (alpha).
· BiocProject - An R package for integrating PEPs with other data structures (alpha).
· geofetch - GEO/SRA data download tool that can build portable encapsulated projects (python).
· dnameth_pipelines - Pipelines for Whole Genome and Reduced Representation Bisulfite-seq.
· rnapipe - Pipeline for RNA-seq data.
· pepatac - Pipeline for ATAC-seq data.
Data analysis software
· pararead - Parallel processing of sequence reads (python).
· MIRA - Bioconductor package for inferring regulatory activity from DNA methylation.
· LOLA - Genomic Locus Overlap Analysis (R). Enrichment of genomic ranges.
· COCOA - Coordinate Covariation Analysis (R). Identifying sources of intersample variation using PCA and region sets for genomic coordinate-based data.
· simpleCache - Fast caching (R).
· dipPeak - A peak caller for DNase data (R).
Web resources and services
- Regulatory Elements Database - A database of DNase hypersensitivity data
- Ewing Sarcoma Epigenome Resources - Comprehensive epigenome mapping of Ewing sarcoma.
- Region Databases - Curated databases of region sets for use with LOLA and other tools.
- 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
|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||2012||GSE54908|