Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

SIB course on single cell transcriptomics by mostly using the Seurat pipeline

Single cell RNA sequencing analysis course

Count bases in BAM/CRAM files

accessory scripts for processing varscan somatic/copynumber outputs.

bam-readcount parser

A set of tools to annotate VCF files with expression and readcount data

Platypus Variant Caller

Variant calling and somatic mutation/CNV detection for next-generation sequencing data

Application for making ENCODE Blacklists

Genome Data Analytics (DSSC 2021)

Extracting mutational signatures via LASSO. The manuscript of the method is published on PLOS Computational Biology and available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journ…

FInding REliable Variants without ArTifacts

cython + htslib == fast VCF and BCF processing

A Variant Call Format reader for Python.

This repository was used to contain the tutorials of telemere length calculation for single cell DNA-seq data.

Telomerecat: The telomere computational analysis tool

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

Fast Gene Set Enrichment Analysis

Estimates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck (OU) models that allow the strength of selection and drift to var…