Stars
R package for detecting doublets in single-cell RNA sequencing data
Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
plotthis is an R package that is built upon ggplot2 and other plotting packages.
scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing and spatial data in an easy and efficient way.
Powerful system-level package manager for Linux, macOS and Windows written in Rust – building on top of the Conda ecosystem.
A Bayesian model for compositional single-cell data analysis
📄 Awesome CV is LaTeX template for your outstanding job application
Inferring and visualizing clonal evolution in multi-sample cancer sequencing
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…
Fast method for inferring cancer clonal population structure from SNV data.
Precision HLA typing from next-generation sequencing data
mhcflow: Modern style HLA typing for class I and II alleles
Detect loss of heterozygosity (LOH) in the MHC in tumor.
Somatic copy variant caller (CNV) for next generation sequencing
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
Copy number variant detection from targeted DNA sequencing
All-FIT - Allele-Frequency-based Imputation of Tumor Purity
Copy number calling and variant classification using targeted short read sequencing
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Tools for working with genomic and high throughput sequencing data.
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
Converts bam or cram files to fastq format and does quality control.