README

DEploid-dev README

Programs

• DEploid [C++]
• DEploid-r [R, C++]
• DEploid-py [Python, C++]

Utilities and extensions

• DEploid-Utilities [R]
• DEploid-ShinyApp [R]

Benchmark experiment and etc

These repositories contains scripts and benchmark analysis for different versions of DEploid

• DEploid-IBD-Benchmark (consider to rename)
• DEploid-IBD-Benchmark-in_silico_field
• DEploid-Lasso-Benchmark
• DEploid-Bestpractices-Benchmark-mixed4s

Benchmark Data

These data are repeated used in testing performance and benchmarking DEploid development

• DEploid-Data-Benchmark-in_silico_field
• DEploid-Data-Benchmark-in_silico_lab_mixed_4s

Pipelines

• pf3k-IBD-deconvolution
• pf6-deconvolution

Paper materials

• dEploidPaper (Bioinfomatics)
• mixedIBD (biorxiv)
• coming soon (for Unknown journal DEploid-LASSO and DEploid-BEST)

Paper supplementary materials

• DEploid-Supplementary-Materials
• mixedIBD-Supplement (https://github.com/mcveanlab/mixedIBD-Supplement)