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325 search results found

Awesome Single Cell ⭐ 2,784

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Single Cell Best Practices ⭐ 544

https://www.sc-best-practices.org

Awesome Omics ⭐ 536

A collection of awesome things regarding all omics.

Scrna Seq_notes ⭐ 478

A list of scRNA-seq analysis tools

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

Single Cell Pseudotime ⭐ 367

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

R package for integrating and analyzing multiple single-cell datasets

Pyscenic ⭐ 321

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

Scrna Tools ⭐ 295

Table of software for the analysis of single-cell RNA-seq data.

Graph-linked unified embedding for single-cell multi-omics data integration

Scarches ⭐ 294

Reference mapping for single-cell genomics

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

R toolkit for the analysis of single-cell chromatin data

Octopus ⭐ 285

Bayesian haplotype-based mutation calling

DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis

Immunarch ⭐ 256

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

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

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

Single cell perturbation prediction

Celltypist ⭐ 202

A tool for semi-automatic cell type classification

Single Cell Papers With Code ⭐ 193

Papers with code for single cell related papers

Pagoda2 ⭐ 191

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

Youtubetutorials ⭐ 180

Sccatch ⭐ 171

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

R package for analyzing single-cell RNA-seq data

Omicverse ⭐ 159

A python library for multi omics included bulk and single cell RNA-seq analysis.

Dittoseq ⭐ 153

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

Sccustomize ⭐ 142

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Single cell analysis in the browser

Tidyseurat ⭐ 131

Seurat meets tidyverse. The best of both worlds.

Vitessce ⭐ 124

Vitessce is a visual integration tool for exploration of spatial single-cell experiments.

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

Scrna.seq.datasets ⭐ 121

Collection of public scRNA-Seq datasets used by our group

Scrnaseq ⭐ 119

A single-cell RNAseq pipeline for 10X genomics data

Ecotyper ⭐ 118

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

Scdblfinder ⭐ 118

Methods for detecting doublets in single-cell sequencing data

Generate high quality, publication ready visualizations for single cell transcriptomics data.

Alevin Fry ⭐ 115

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Decoupler Py ⭐ 112

Python package to perform enrichment analysis from omics data.

Deepcpg ⭐ 108

Deep neural networks for predicting CpG methylation

Anndata2ri ⭐ 104

Convert between AnnData and SingleCellExperiment

Wave_clus ⭐ 102

A fast and unsupervised algorithm for spike detection and sorting using wavelets and super-paramagnetic clustering

Powsimr ⭐ 102

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

Seurat Data ⭐ 101

Dataset distribution for Seurat

Liana Py ⭐ 99

LIANA+: an all-in-one framework for cell-cell communication

Infercnvpy ⭐ 97

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

Too Many Cells ⭐ 95

Cluster single cells and analyze cell clade relationships with colorful visualizations.

Scdeepsort ⭐ 93

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

Scatac Benchmarking ⭐ 92

Benchmarking computational single cell ATAC-seq methods

Cellsnp Lite ⭐ 89

Efficient genotyping bi-allelic SNPs on single cells

mgatk: mitochondrial genome analysis toolkit

Multiome GRN inference.

Tools for single-cell data processing

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

Multi-omic single-cell optimal transport tools

marker-based purification of cell types from single-cell RNA-seq datasets

Cell_blast ⭐ 74

A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.

Scrnaseqpipeline ⭐ 73

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

Curatedatlasqueryr ⭐ 70

Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.

Topometry ⭐ 69

Systematically learn and evaluate manifolds from high-dimensional data

Perturbation Analysis in the scverse ecosystem.

Singlecellhaystack ⭐ 68

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Multi-sample Unified Discriminant ANalysis

Rapids_singlecell ⭐ 66

Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

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.

Scatac Pro ⭐ 64

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Cirrocumulus ⭐ 63

Bring your single-cell data to life

Single Cell Training ⭐ 63

SIB course on single cell transcriptomics by mostly using the Seurat pipeline

Cut Runtools 2.0 ⭐ 62

CUT&RUN and CUT&Tag data processing and analysis

Covid 19 Rna Seq Datasets ⭐ 61

A repository for sharing information on available COVID-19 RNA-Seq datasets

Demultiplexing pooled scRNA-seq data with or without genotype reference

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph

trajectory inference

Scavenge ⭐ 60

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

Dynverse ⭐ 58

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

Cardelino ⭐ 57

Clone identification from single-cell data

Scperturb ⭐ 56

scPerturb: A resource and a python/R tool for single-cell perturbation data

Fast visualization tool for large-scale and high dimensional single-cell data

Multinichenetr ⭐ 56

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Kallistobustools ⭐ 55

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

Conditional out-of-distribution prediction

Statistical approach for removing unwanted variation from multiple single-cell datasets

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

Spatial-Linked Alignment Tool

Simulating single-cell data using gene regulatory networks 📠

Deep learning for single-cell transcript counts

Monopogen ⭐ 50

SNV calling from single cell sequencing

Magma_celltyping ⭐ 50

Find causal cell-types underlying complex trait genetics

Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.

Nebulosa ⭐ 50

R package to visualize gene expression data based on weighted kernel density estimation

Cite Seq Count ⭐ 50

A tool that allows to get UMI counts from a single cell protein assay

single cell Flux Estimation Analysis (scFEA) Try the below web server!

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Related Searches

R Single Cell (121)

Python Single Cell (99)

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Bioinformatics Single Cell (76)

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