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awesome-single-cell

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

bcd

Visualization and analysis of single-cell RNA-seq data by alternative clustering

bindsc

Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data

ccadge

Detection of disease-associated genes from single cell data

cyclum

Identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations

cyclum-demo

A self-contained demo of Cyclum, ships with the mESC data

cyclum-gp

A more flexible version of Cyclum, utilizing GPLVM with periodic kernel

cytospill

A statistical approach that reduces spillover noise in the mass cytometry (CyTOF) data

data-analysis-of-variant-functional-effects

Data analysis for manuscript submission

epinb

Efficient and interpretable HLA-I binding peptide identification

gsdensity

human-cell-atlas

invax_manuscript

Scripts/Codes for INVAX project paper

lad

Visualization and analysis of single-cell RNA-seq data by alternative clustering

mcl_ml_project

Code for models and visualizations for HHill's MCL ML project.

medalt

Inference of Minimal Event Distance Aneuploidy Lineage Tree based on single cell copy number profile

metaflux

monopogen

SNV calling from single cell sequencing

monovar

Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data

nk_cebpd_manuscript

Scripts/Codes for NK CEBPD paper

novobreak

A de novo genome breakpoint sequence assembly algorithm

novornabreak

scmarker

Marker gene selection from scRNA-seq data

scmer

Marker Selection by matching manifolds and elastic net

sensei

Sample size estimation for single cell studies

sifit

Reconstructing phylogenetic tree from noisy mutation profile of single cells

stratified-tests-for-seurat

Stratified statistic hypothesis tests for Seurat

texomer

Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data

tf-rna-atac

Clustering transcription factors based on expression and chromatin openness

transition-cells-identification