Kieran R Campbell

clonealign. Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data

ouija. Descriptive probabilistic marker gene approach to single-cell pseudotime inference

switchde. Inference of switch-like differential expression along single-cell trajectories

embeddr. This repository is retired software

curver-python. Curve reconstruction from noisy points (python)

ouijaflow. Probabilistic single-cell pseudotime with Edward+Tensorflow

phenopath. Genomic trajectories (pseudotimes) in the presence of heterogenous environmental and genetic backgrounds

pseudogp. Probabilistic pseudotime for single-cell RNA-seq data

gpseudotime. Bayesian Gaussian Process Latent Variable Models for pseudotime inference in single-cell RNA-seq data

mfa. Probabilistic inference of single-cell bifurcations

r-workshop-march-2019. R workshop on single cell genomics at BC Cancer March 2019

scrnaseq-digestion-paper. BC Cancer single-cell RNA-seq digestion method paper

autosmk. Autogenerate templates for Snakemake rules and R scripts

blog-notebooks. IPython notebooks and R markdowns for blog

camlab-website. Hugo website for camlab Toronto

clonealign-pipeline. A pipeline to process scRNA-seq (10X chromium) and scDNA-seq CNV data and infer clone-specific expression using clonealign

cellassign. Automated, probabilistic assignment of cell types in scRNA-seq data

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

pseudogp-paper. Reproducible analysis for "Order under uncertainty: on the robustness of differential expression analysis using probabilistic models for pseudotime inference"

stan-workshop. STAN workshop for GMS students

curver. Curve reconstruction from noisy points

ouija-paper. Reproducible analysis for Ouija paper

bmfa. Modelling bifurcations in genomics data using Bayesian hierarchical mixture of factor analysers

mallard. Data Acquisition for the CRIS experiment at ISOLDE

snvworkflow. Python