Kharchenko Lab

Pinned Repositories

Baysor
Bayesian Segmentation of Spatial Transcriptomics Data
Language:Julia158 10 13632
cacoa
Single-cell Case Control Analysis
Language:R48 9 438
conos
R package for the joint analysis of multiple single-cell RNA-seq datasets
Language:R202 12 9639
dropEst
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
Language:C++88 15 13242
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:R172 9 19123
pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
Language:JavaScript218 16 11647
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:R54 4 142
vrnmf
Volume-regularized NMF
Language:R17 3 14

Kharchenko Lab's Repositories

kharchenkolab/pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
Language:JavaScript218 16 11647
kharchenkolab/conos
R package for the joint analysis of multiple single-cell RNA-seq datasets
Language:R202 12 9639
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
Language:R172 9 19123
kharchenkolab/Baysor
Bayesian Segmentation of Spatial Transcriptomics Data
Language:Julia158 10 13632
kharchenkolab/dropEst
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
Language:C++88 15 13242
kharchenkolab/scITD
Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
Language:R54 4 142
kharchenkolab/cacoa
Single-cell Case Control Analysis
Language:R48 9 438
kharchenkolab/vrnmf
Volume-regularized NMF
Language:R17 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:R8 3 21
kharchenkolab/gpsFISH
Optimization of gene panels for targeted spatial transcriptomics
Language:R7 2 111
kharchenkolab/scistreer
R/Rcpp implementation of the ScisTree algorithm
Language:R7 3 12
kharchenkolab/BaysorAnalysis
Analysis for the Baysor paper
Language:Jupyter Notebook5 4 42
kharchenkolab/scLiTr
Repository for the scLiTr (single-cell Lineage Tracing analysis) python package
Language:Python4 2 00
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/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/cellAdmix
Evaluating and correcting cell admixtures in imaging-based spatial transcriptomics data
Language:Jupyter Notebook0 1 00
kharchenkolab/clonal-atlas-paper
The repository with the code and analysis for the paper [Erickson et al]
Language:Jupyter Notebook
kharchenkolab/GraphPriorKMeans
Language:Julia
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