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Search results for single cell analysis

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64 search results found

Cellchat ⭐ 548

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

Seurat Wrappers ⭐ 268

Community-provided extensions to Seurat

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.

Snapatac ⭐ 227

Analysis Pipeline for Single Cell ATAC-seq

Pycomplexheatmap ⭐ 182

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

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

Harmonypy ⭐ 116

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

Dynmethods ⭐ 107

A collection of 50+ trajectory inference methods within a common interface 📥📤

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

Too Many Cells ⭐ 95

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

Honeybadger ⭐ 94

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

Context specific and dynamic gene regulatory network reconstruction and analysis

Cellchat ⭐ 76

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

Celescope ⭐ 73

Single Cell Analysis Pipelines

Scavenge ⭐ 60

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

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

Simulating single-cell data using gene regulatory networks 📠

Spatial-Linked Alignment Tool

Nebulosa ⭐ 50

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

Spatial Single-Cell Analysis Toolkit

Scissor package

Randomly ⭐ 33

A Library for Denoising Single-Cell Data with Random Matrix Theory

Umi Normalization ⭐ 26

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

Seuratv3wizard ⭐ 26

A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3

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

Split Seq_demultiplexing ⭐ 25

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

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)

Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

<<------ Use SnapATAC!!

Pseudodynamics ⭐ 23

Dynamic models for single-cell RNA-seq time series.

Accurate and fast cell marker gene identification with COSG

Singlecell ⭐ 22

Code repository for single cell RNA-seq

Marker Selection by matching manifolds and elastic net

An analytics package for single cell data

BEER: Batch EffEct Remover for single-cell data

Clustermap ⭐ 18

ClusterMap for multi-scale clustering analysis of spatial gene expression

Demuxalot ⭐ 17

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

Sckinetics ⭐ 15

Code for scKINETICS (ISMB 2023)

Deciphering driver regulators of cell fate decisions from single-cell RNA-seq data

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

An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

SCASA: Single cell transcript quantification tool

Transmorph ⭐ 10

Computational framework for dataset integration

Scpretrain ⭐ 10

scPretrain: Multi-task self-supervised learning for cell type classification

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics

Genomics.ai ⭐ 9

a web application to annotate and visualise single-cell sequencing data using neural networks

SIMBA: SIngle-cell eMBedding Along with features

VEGA: VAE Enhanced by Gene Annotations

represent each cell in UMAP plots as a pie chart

Provisional_cell_ontology ⭐ 7

Draft cell type definitions from data - candidates for inclusion in CL

Seuratwizard ⭐ 7

This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.

The CanceR Single Cell ExpressioN Toolkit one-line-command applications.

Single-cell alignment

Cytocommunity ⭐ 7

A spatial omics data analysis tool that enables both unsupervised and supervised discovery of complex tissue cellular neighborhoods from cell phenotypes.

resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments

CALISTA: Clustering And Lineage Inference in Single Cell Transcriptional Analysis

A reference-based solution for single-cell analysis

Related Searches

R Single Cell Analysis (28)

Python Single Cell Analysis (26)

1-64 of 64 search results

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