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Search results for scrna seq

142 search results found

Scvi Tools ⭐ 1,120

Deep probabilistic analysis of single-cell and spatial omics data

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

Cellxgene ⭐ 544

An interactive explorer for single-cell transcriptomics data

Scrna Seq_notes ⭐ 478

A list of scRNA-seq analysis tools

Harmony ⭐ 460

Fast, sensitive and accurate integration of single-cell data with Harmony

Dynamo Release ⭐ 383

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

Scrna Tools ⭐ 295

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

Scarches ⭐ 294

Reference mapping for single-cell genomics

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

Single cell perturbation prediction

Celltypist ⭐ 202

A tool for semi-automatic cell type classification

Splatter ⭐ 195

Simple simulation of single-cell RNA sequencing data

muon is a multimodal omics Python framework

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

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

Palantir ⭐ 184

Single cell trajectory detection

Maestro ⭐ 181

Single-cell Transcriptome and Regulome Analysis Pipeline

Scrnatoolvis ⭐ 169

Useful functions to make your scRNA-seq plot more cool!

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

Tangram ⭐ 153

Spatial alignment of single cell transcriptomic 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.

Souporcell ⭐ 134

Clustering scRNAseq by genotypes

Kb_python ⭐ 132

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

Zellkonverter ⭐ 112

Conversion between scRNA-seq objects

Cellxgene_vip ⭐ 111

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

Scdeepsort ⭐ 93

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

Interactive 3d Plotting In Seurat 3.0.0 ⭐ 88

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

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

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

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

Symphony ⭐ 73

Efficient and precise single-cell reference atlas mapping with Symphony

Bulk2space ⭐ 68

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

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.

Cirrocumulus ⭐ 63

Bring your single-cell data to life

Single-cell Hierarchical Poisson Factorization

Demultiplexing pooled scRNA-seq data with or without genotype reference

Doubletdetection ⭐ 60

Doublet detection in single-cell RNA-seq data.

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

Multinichenetr ⭐ 56

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

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

Imputation method for scRNA-seq based on low-rank approximation

Cellpypes ⭐ 48

Cell type pipes for R

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

Scclusteval ⭐ 45

Single Cell Cluster Evaluation

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Cellhint ⭐ 44

A tool for semi-automatic cell type harmonization and integration

Scclustviz ⭐ 42

Explore and share your scRNAseq clustering results

Discover differential transcript usage from polyA-captured single cell RNA-seq data

Cellxgene Gateway ⭐ 40

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

Deep Embedding for Single-cell Clustering

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

Scrna Recom ⭐ 36

collected resource for scRNA-seq analysis

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.

A portable and fast single cell type identifier

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

Interactive software tool for the assignment of cell types in single-cell studies.

Fastq_utils ⭐ 29

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

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

A tool for fast and accurate summarizing of variant calling format (VCF) files

Mudskipper ⭐ 25

A tool for projecting genomic alignments to transcriptomic coordinates

Scib Reproducibility ⭐ 25

Additional code and analysis from the single-cell integration benchmarking project

Split Seq_demultiplexing ⭐ 25

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

R package IReNA

Principal Component Analysis All in One

Fishpond ⭐ 23

Differential expression and allelic analysis, nonparametric statistics

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.

Northstar ⭐ 23

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

Cellguide ⭐ 22

🧭 Navigate single-cell RNA-seq datasets in your web browser.

Clustergrammer2 Notebooks ⭐ 22

Examples using Clustergrammer2 to explore high-dimensional datasets.

Pathogentrack ⭐ 22

A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.

Single-cell Transcriptome and Regulome Analysis Pipeline.

scGSVA: Perform GSVA for single cell RNA seq

Cell2sentence Ft ⭐ 21

Cell2Sentence turns scRNA-seq data into text for LLM training.

Scgeatoolbox ⭐ 21

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

Cellenium ⭐ 20

Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data (single-cell RNA sequencing).

Accurate and fast cell marker gene identification with COSG

Symphonypy ⭐ 19

Port of symphony algorithm of single-cell reference atlas mapping to Python

Cellrouter ⭐ 19

Reconstruction of complex single-cell trajectories using CellRouter

Devcellpy ⭐ 18

devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing.

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

Singlecell_neuroseq_paper ⭐ 18

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

BEER: Batch EffEct Remover for single-cell data

R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-cell analytic work flows.

Demuxalot ⭐ 17

Reliable, scalable and demultiplexing for single-cell RNA sequencing. Improves genotypes with Expectation-Maximization

R package for analysing single cell data

Visium Clustergrammer2 ⭐ 14

Spatial Transcriptomics Dashboard

Mudataseurat ⭐ 14

.h5mu files interface for Seurat

The R package scCODE, a platform for data-specific DE gene detection for scRNA-seq data

Bgeedb_r ⭐ 13

Source code of the R packge BgeeDB to use data from the Bgee database

Robustsinglecell ⭐ 13

Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.

SHARP: Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection

Assessing the purity of single cell population

Scpca Nf ⭐ 11

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

Scinsight ⭐ 11

Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data

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