Accessible and interoperable whole slide image analysis

Electronic Health Record Analysis with Python.

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

🧬Genomes to proteins, multi-level visualization library

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…

VirusScan Pipeline

Battenberg R package for subclonal copynumber estimation

C library for reading virtual slide images

Utility functions for FACETS

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

software version control visualization

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

Pipeline for generating RNAseq-based cancer patient reports

redevelopment of this powerful tool for MAF, add CNV annotations

A comprehensive data mining and visualization framework for tabular aging features in clinical and omics assays.

An annotation package for ggplot plot

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

Generate your GitHub's Stats in SVG

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.