Kharchenko Lab

Pinned Repositories

Baysor
Bayesian Segmentation of Spatial Transcriptomics Data
Language:Julia139 11 10927
cacoa
Single-cell Case Control Analysis
Language:R44 9 437
conos
R package for the joint analysis of multiple single-cell RNA-seq datasets
Language:R189 13 9438
dropEst
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
Language:C++84 15 13243
hahmmr
Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq
Language:R13 3 20
numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
Language:R157 9 17122
pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
Language:JavaScript193 18 11246
sccore
Core utilities for single-cell RNA-seq
Language:R12 8 43
scITD
Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
Language:R34 4 120
vrnmf
Volume-regularized NMF
Language:R18 3 14

Kharchenko Lab's Repositories

kharchenkolab/pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
Language:JavaScript193 18 11246
kharchenkolab/conos
R package for the joint analysis of multiple single-cell RNA-seq datasets
Language:R189 13 9438
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
Language:R157 9 17122
kharchenkolab/Baysor
Bayesian Segmentation of Spatial Transcriptomics Data
Language:Julia139 11 10927
kharchenkolab/dropEst
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
Language:C++84 15 13243
kharchenkolab/cacoa
Single-cell Case Control Analysis
Language:R44 9 437
kharchenkolab/scITD
Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
Language:R34 4 120
kharchenkolab/vrnmf
Volume-regularized NMF
Language:R18 3 14
kharchenkolab/hahmmr
Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq
Language:R13 3 20
kharchenkolab/sccore
Core utilities for single-cell RNA-seq
Language:R12 8 43
kharchenkolab/N2R
R extensions to N2 implementing approximate nearest neighbor search methods
Language:C++10 5 33
kharchenkolab/leidenAlg
Implements the Leiden algorithm via an R interface
Language:C9 4 144
kharchenkolab/NumbatAnalysis
Analysis scripts and notebooks for Numbat paper
Language:R7 3 21
kharchenkolab/gpsFISH
Optimization of gene panels for targeted spatial transcriptomics
Language:R6 2 101
kharchenkolab/BaysorAnalysis
Analysis for the Baysor paper
Language:Jupyter Notebook5 4 42
kharchenkolab/cap-example
An example of proposed CAP annotation view
5 7 0
kharchenkolab/scistreer
R/Rcpp implementation of the ScisTree algorithm
Language:R5 3 01
kharchenkolab/dropestr
Preprocessing of Droplet-based Single-Cell RNA-seq Data
Language:R4 4 02
kharchenkolab/AllenBrain_AnnData
Instructions on how to convert Allen Brain Atlas data into AnnData files
Language:Python2 4 1
kharchenkolab/cacoaAnalysis
Analysis for the Cacoa paper
Language:R2 3 0
kharchenkolab/conosViz
Shiny App to Visualize Dendrograms and Heatmaps from Conos
Language:R2 4 01
kharchenkolab/conosPanel
Package with data used by conos: panel of four samples with 3000 cells each
Language:R1 4 0
kharchenkolab/drat
Drat repo with R packages
1 5 0
kharchenkolab/p2data
Package with data used by pagoda2, 3000 bone marrow cells
Language:R1 3 1
kharchenkolab/ScisTree
Cell tree inference and genotype calling from noisy single cell data
Language:C++1 1 0
kharchenkolab/simulatedNMF
Package with data used by vrnmf, simulated NMF matrices
Language:R1 3 0
kharchenkolab/cloud-sdk-docker
Docker image with all the components of the Google Cloud SDK
Language:Dockerfile1 0
kharchenkolab/mouseCochlea
processing code for Tasdemir-Yilmaz et al. "Diversity of developing peripheral glia revealed by single cell RNA sequencing"
Language:HTML3 0
kharchenkolab/slideseqde
Language:R3 0
kharchenkolab/thymus-mesenchyme
Code and notebooks for Gustafsson et al. scRNA-Seq analysis of thymic mesenchymal cells
Language:Jupyter Notebook4 01