Stars
Modular Nextflow pipeline for small RNA-seq analysis
MethyLYZR: a Naïve Bayesian framework for rapid brain tumor classification from sparse epigenomic data
DNA methylation-based classification of central nervous system tumours
Pipeline to replicate Katsman et. al fragmentomics results
Profiling of transcription factor binding sites in cell-free DNA
cfNOMe toolkit. Includes tools for nucleosome occupancy studies as well as methylation deconvolution of cfDNA tissues-of-origin
FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA