kharchenkolab Goto Github PK

allenbrain_anndata

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

baysor

Bayesian Segmentation of Spatial Transcriptomics Data

baysoranalysis

Analysis for the Baysor paper

cacoa

Single-cell Case Control Analysis

cacoaanalysis

Analysis for the Cacoa paper

cap-example

An example of proposed CAP annotation view

cloud-sdk-docker

Docker image with all the components of the Google Cloud SDK

conos

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

conospanel

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

conosviz

Shiny App to Visualize Dendrograms and Heatmaps from Conos

drat

Drat repo with R packages

dropest

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

dropestr

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

gitea

Git with a cup of tea, painless self-hosted git service

gpsfish

Optimization of gene panels for targeted spatial transcriptomics

hahmmr

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

leidenalg

Implements the Leiden algorithm via an R interface

mousecochlea

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

n2r

R extensions to N2 implementing approximate nearest neighbor search methods

numbat

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

numbatanalysis

Analysis scripts and notebooks for Numbat paper

p2data

Package with data used by pagoda2, 3000 bone marrow cells

pagoda2

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

pysccnv

sccore

Core utilities for single-cell RNA-seq

scistree

Cell tree inference and genotype calling from noisy single cell data

scistreer

R/Rcpp implementation of the ScisTree algorithm

scitd

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

simulatednmf

Package with data used by vrnmf, simulated NMF matrices

slideseqde