calcium imaging

  • CaGenNet: single-cell generative models for calcium imaging data

genetic variation

  • snputils: processing genetic variation and population structure
  • MlcbFuses2025: Multimodal genotype-phenotype prediction of Huntington’s disease age of onset.

phenotype prediction

  • DIAGNNAD: graph neural network based AD diagnosis prediction

dna methylation

  • CpelNano: DNA methylation landscape analysis of nanopore sequencing data
  • CpelTdm: targeted differential DNA methylation analysis
  • CpelAsm: haplotype allele-specific DNA methylation analysis
  • informME: information-theoretic pipeline for DNA methylation analysis of WGBS data

mobile genetic elements

  • DIVE: reference-free de novo discovery of diversity-generating & mobile genetic elements

genome & transcriptome

  • HiMMe: pipeline to assess NGS data reliability using hidden Markov models

nucleosome positioning

  • NucSeq: pipeline to analyze MNaseq-seq data