Stars
A curated collection of Nextflow implementation patterns
Turn an existing conda environment into a Singularity container
Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples a…
Mixed-effect model to test differences in cell type proportions from single-cell data, in R
A free and open-source pedigree tool by PhenoTips®
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
A package that makes Julia take advantage of cool terminal emulator features.
Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
RTG Tools: Utilities for accurate VCF comparison and manipulation
phasing and Allele Specific Expression from RNA-seq
Somatic mutation calling on moderately deep WES data using GATK/MuTect
caravagnalab / ctree
Clone trees for Cancer Evolution studies from bulk sequencing data.
Log-normal-Poisson regression model from Hess et al. 2019
HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, a…
dN/dS methods to quantify selection in cancer and somatic evolution
R data package for annotating/converting Gene IDs
C++ Implementation of a standard bloom filter, using MurmurHash (v2)