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31 search results found

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Single Cell Papers With Code ⭐ 193

Papers with code for single cell related papers

Palantir ⭐ 184

Single cell trajectory detection

Souporcell ⭐ 134

Clustering scRNAseq by genotypes

Quantifying experimental perturbations at single cell resolution

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks

Supercell ⭐ 44

Coarse-graining of large single-cell RNA-seq data into metacells

Scclustviz ⭐ 42

Explore and share your scRNAseq clustering results

Harmony framework for connecting scRNA-seq data from discrete time points

Data-driven Network-based Bayesian Inference of Drivers

Statistical quality evaluation of dimensionality reduction algorithms

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

Split Seq_demultiplexing ⭐ 25

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Northstar ⭐ 23

Single cell type annotation guided by cell atlases, with freedom to be queer

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

Cell type matching in single-cell RNA-sequencing data using FR-Match

Recurrent Variational Auto gene encoder

R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single-cell CRISPR screening data.

R package for single-cell RNA-sequencing analysis

scRNA analysis pipeline

Projectsvr ⭐ 9

A package for reference mapping and nice visualization

Pancreas_ductal_scrnaseq ⭐ 9

The following repository contains code for all scRNAseq analysis and visualization performed in the paper: Single cell resolution analysis of the human pancreatic ductal progenitor cell niche

Granular Functional Filtering (Gruffi) to isolate stressed cells

Simple implementation of different single cell RNA-seq methods

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

The Cornell Single-Cell Muscle Project (scMuscle) aims to collect, analyze and provide to the research community skeletal muscle transcriptomic data

scSPARKL is an Apache spark based pipeline for performing variety of preprocessing and downstream analysis of scRNA-seq data.

Scrna_seq Analysis ⭐ 5

scRNA analysis of public dataset on bladder cancer

Scpipeline ⭐ 5

Single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports

Intercellular communication analysis for scRNA-seq data

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Scrna Seq Analysis Gene Expression Profiles (3)

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