Stars
Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
Nextflow pipeline to preprocess perturb-seq/MAESTER data.
LuLu is the free open-source macOS firewall
MiTo: MT-SNVs based single-cell lineage tracing in python
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
accessory scripts for processing varscan somatic/copynumber outputs.
A set of tools to annotate VCF files with expression and readcount data
Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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…
jamescasbon / PyVCF
Forked from jdoughertyii/PyVCFA 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