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academic

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

blog

my blog sources

bnpc

Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates

cello

CELLO - Cancer EvoLution toolbox for LOngitudinal data

clonalgrowthsimulator_ssa

Gillespie simulator of clonal growth

cnape

[Source] CNAPE: A Software for Copy Number Alteration Prediction from Gene Expression in Human Cancers

curatedtcgadata

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

demon_model

A deme-based, spatially explicit model of intra-tumour population genetics

dndscv

dN/dS methods to quantify selection in cancer and somatic evolution

ffpe-filter-legacy

infercnv

Inferring CNV from Single-Cell RNA-Seq

lineage-dynamics

mobster

Model-based subclonal deconvolution from bulk sequencing.

mutationalpatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

pastri

phylogicndt

phylom

Tumor Phylogeny Topology Inference via Deep Learning

pvactools

revolver

REVOLVER - Repeated Evolution in Cancer

scimet

scoup

SCOUP is a probabilistic model to analyze single-cell expression data during differentiation

scrnapipeline

Single Cell RNA-seq Pipeline

siapopr

R wrappers for SIApop

single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

starter-hugo-academic

🎓 创建一个学术网站. Easily create a beautiful academic résumé or educational website using Hugo, GitHub, and Netlify.

tcgamutations

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

themillerlab

The Miller Lab Website

themillerlab-website

New Website 2-29-2020

titancna

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer