Pinned Repositories
cellscape
Visualization tool for integrating single cell phylogeny with genomic content to clearly display evolutionary progression and tumour heterogeneity.
hmmcopy_utils
Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.
MultiModalMuSig.jl
A Julia package for extracting mutation signatures using topic models
mutationseq
Software for somatic SNV detection using next generation sequencing (NGS) data.
SCRNApipeline
Single Cell RNA-seq Pipeline
scvis
Python package for dimension reduction of high-dimensional biological data.
single_cell_pipeline
Single Cell Analysis Automated Workflow
spectrum-tme
Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"
timescape
Visualization tool for temporal clonal evolution.
wgs
Whole genome workflows
ShahCompBio's Repositories
shahcompbio/scvis
Python package for dimension reduction of high-dimensional biological data.
shahcompbio/cellscape
Visualization tool for integrating single cell phylogeny with genomic content to clearly display evolutionary progression and tumour heterogeneity.
shahcompbio/xseq
A hierarchical Bayesian approach to assess functional impact of mutations on gene expression in cancer.
shahcompbio/drivernet
Package to predict functional important driver genes in cancer by integrating genome data and transcriptome data.
shahcompbio/snvmix
Software to detect single nucleotide variants from next generation sequencing data.
shahcompbio/LTM
Latent tree models for phylogenetic inference of single-cell data
shahcompbio/apolloh
Hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.
shahcompbio/cel
Front-end library visualization for Colossus
shahcompbio/lyra-website
Docs for Lyra
shahcompbio/postpy
Set of tools to help with post-processing PyClone results.
shahcompbio/scg
Software for inference of clonal genotypes using targeted single cell (nucleus) sequencing.
shahcompbio/smartchipapp
Smart Chip Application for Direct Library Prep
shahcompbio/variant_calling