calcium imaging

• AVAE: autoregressive variational autoencoder for calcium imaging data

genetic variation

• snputils: processing genetic variation and population structure

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

others

• myutils: useful scripts for routinary bioinformatics