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Search results for single cell genomics

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45 search results found

Seurat ⭐ 2,025

R toolkit for single cell genomics

Scvi Tools ⭐ 1,120

Deep probabilistic analysis of single-cell and spatial omics data

Squidpy ⭐ 362

Spatial Single Cell Analysis in Python

Scarches ⭐ 294

Reference mapping for single-cell genomics

Cellrank ⭐ 279

CellRank: dynamics from multi-view single-cell data

Seurat Wrappers ⭐ 268

Community-provided extensions to Seurat

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

Single cell perturbation prediction

Palantir ⭐ 184

Single cell trajectory detection

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.

Snapatac2 ⭐ 133

Single-cell epigenomics analysis tools

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

Seurat Disk ⭐ 111

Interfaces for HDF5-based Single Cell File Formats

Seurat Data ⭐ 101

Dataset distribution for Seurat

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

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.

A Shiny web app for mapping datasets using Seurat v4

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

Single_cell_portal_core ⭐ 60

Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

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.

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

Celldancer ⭐ 46

Predict RNA velocity through deep learning

Cloud-based single-cell copy-number variation analysis tool

Convert Seurat objects to 10x Genomics Loupe files.

Single_cell_portal ⭐ 41

Tutorials, workflows, and convenience scripts for Single Cell Portal

An R-based interface for loom files

Pyrovelocity ⭐ 31

𝒫robabilistic modeling of RNA velocity ⬱

A deep learning architecture for robust inference and accurate prediction of cellular dynamics

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

Big data Regression for predicting DNase I hypersensitivity

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

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

Seurat.utils ⭐ 19

Various utility functions for Seurat single-cell analysis

Robustsinglecell ⭐ 13

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

Apackoftheclones ⭐ 10

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.

Genomics.ai ⭐ 9

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

The Broad Institute Single Cell Rna Seq Data Set ⭐ 9

Visualize cancer genomes with FAIR single-cell RNA-seq data

Amp_phase1_ra ⭐ 8

🌾 Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.

Singlecellhaystack Py ⭐ 8

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

SCGV is an interactive graphical tool for single-cell genomics data, with emphasis on single-cell genomics of cancer

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.

Timshel 2020 ⭐ 6

Code to reproduce analysis and figures for 'Genetic mapping of etiologic brain cell types for obesity' (Timshel, eLife 2020)

Codes for paper: AWGAN: A Powerful Batch Effect Removal Model for scRNA-seq Data

R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.

Treecortreat ⭐ 5

Related Searches

R Single Cell Genomics (17)

Python Single Cell Genomics (17)

Scrna Seq Single Cell Genomics (12)

Jupyter Notebook Single Cell Genomics (10)

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