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single-cell-genomics

Here are 97 public repositories matching this topic...

satijalab / seurat

R toolkit for single cell genomics

cran single-cell-genomics single-cell-rna-seq human-cell-atlas

Updated Oct 25, 2024
R

scverse / scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse

Updated Nov 25, 2024
Python

squidpy

scverse / squidpy

Spatial Single Cell Analysis in Python

data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy

Updated Nov 26, 2024
Python

zhanghao-njmu / SCP

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

scrna-seq shiny-apps single-cell shinyapps single-cell-genomics single-cell-rna-seq single-cell-analysis single-cell-atac-seq seurat single-cell-omics scrna-seq-analysis single-cell-sequencing shiny-app scanpy scatac-seq anndata scrna-pipeline seurat-objects single-cell-pipeline

Updated May 21, 2024
R

cellrank

theislab / cellrank

CellRank: dynamics from multi-view single-cell data

data-science machine-learning bioinformatics genetics trajectory-generation markov-chains manifold-learning single-cell-genomics single-cell-rna-seq cell-fate-transitions fuzzy-clustering-analyses rna-velocity cell-fate-determination

Updated Oct 7, 2024
Python

theislab / scarches

Reference mapping for single-cell genomics

deep-learning scrna-seq data-integration single-cell rna-seq-analysis single-cell-genomics batch-correction multimodal-deep-learning multiomics human-cell-atlas

Updated Oct 27, 2024
Jupyter Notebook

satijalab / seurat-wrappers

Community-provided extensions to Seurat

community single-cell-genomics single-cell-analysis

Updated Nov 22, 2024
R

theislab / scgen

Single cell perturbation prediction

bioinformatics deep-learning generative-model scrna-seq transcriptomics single-cell single-cell-genomics

Updated Jun 19, 2024
Python

kaizhang / SnapATAC2

Single-cell epigenomics analysis tools

single-cell-genomics

Updated Nov 27, 2024
Python

dpeerlab / Palantir

Single cell trajectory detection

markov-chain dimensionality-reduction scrna-seq trajectory-generation diffusion-maps differentiation manifold-learning single-cell-genomics cell-fate-transitions scrna-seq-analysis

Updated Nov 26, 2024
Jupyter Notebook

samuel-marsh / scCustomize

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

visualization ggplot2 customization scrna-seq single-cell single-cell-genomics single-cell-rna-seq seurat

Updated Nov 26, 2024
R

SCpubr

enblacar / SCpubr

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

visualization ggplot2 r data-visualization rstats single-cell single-cell-genomics single-cell-rna-seq publication-quality-plots seurat

Updated Aug 21, 2024
R

mojaveazure / seurat-disk

Interfaces for HDF5-based Single Cell File Formats

hdf5-format single-cell-genomics single-cell-rna-seq

Updated Nov 4, 2023
R

satijalab / seurat-data

Dataset distribution for Seurat

datasets single-cell single-cell-genomics

Updated Nov 4, 2023
R

satijalab / azimuth

A Shiny web app for mapping datasets using Seurat v4

single-cell-genomics single-cell-rna-seq shiny-app

Updated Nov 5, 2024
HTML

yanwu2014 / swne

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

bioinformatics statistical-methods data-visualization dimensionality-reduction single-cell-genomics single-cell-rna-seq nonnegative-matrix-factorization single-cell-analysis single-cell-atac-seq

Updated Aug 2, 2023
R

10XGenomics / loupeR

Convert Seurat objects to 10x Genomics Loupe files.

r-package 10xgenomics single-cell-genomics

Updated Oct 29, 2024
R

parashardhapola / scarf

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.

Updated Oct 23, 2024
Python

theislab / cpa

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.

scrna-seq single-cell-genomics single-cell-rna-seq human-cell-atlas

Updated Aug 14, 2024
Python

calico / scnym

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

rna-seq single-cell single-cell-genomics semi-supervised adversarial-training

Updated Dec 11, 2023
Python

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