Kharchenko Lab

pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

conos

R package for the joint analysis of multiple single-cell RNA-seq datasets

numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

cacoa

Single-cell Case Control Analysis

scITD

Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition

vrnmf

Volume-regularized NMF

hahmmr

Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq

sccore

Core utilities for single-cell RNA-seq

N2R

R extensions to N2 implementing approximate nearest neighbor search methods

leidenAlg

Implements the Leiden algorithm via an R interface

NumbatAnalysis

Analysis scripts and notebooks for Numbat paper

gpsFISH

Optimization of gene panels for targeted spatial transcriptomics

BaysorAnalysis

Analysis for the Baysor paper

cap-example

An example of proposed CAP annotation view

scistreer

R/Rcpp implementation of the ScisTree algorithm

dropestr

Preprocessing of Droplet-based Single-Cell RNA-seq Data

AllenBrain_AnnData

Instructions on how to convert Allen Brain Atlas data into AnnData files

cacoaAnalysis

Analysis for the Cacoa paper

conosViz

Shiny App to Visualize Dendrograms and Heatmaps from Conos

conosPanel

Package with data used by conos: panel of four samples with 3000 cells each

drat

Drat repo with R packages

p2data

Package with data used by pagoda2, 3000 bone marrow cells

ScisTree

Cell tree inference and genotype calling from noisy single cell data

simulatedNMF

Package with data used by vrnmf, simulated NMF matrices

cloud-sdk-docker

Docker image with all the components of the Google Cloud SDK

mouseCochlea

processing code for Tasdemir-Yilmaz et al. "Diversity of developing peripheral glia revealed by single cell RNA sequencing"

slideseqde

thymus-mesenchyme

Code and notebooks for Gustafsson et al. scRNA-Seq analysis of thymic mesenchymal cells