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Search results for python single cell
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single-cell
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77 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.
Phate
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421
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
Pyscenic
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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.
Glue
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294
Graph-linked unified embedding for single-cell multi-omics data integration
Dance
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284
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
Scgen
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215
Single cell perturbation prediction
Celltypist
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202
A tool for semi-automatic cell type classification
Stream
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163
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
Decoupler Py
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112
Python package to perform enrichment analysis from omics data.
Deepcpg
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108
Deep neural networks for predicting CpG methylation
Anndata2ri
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104
Convert between AnnData and SingleCellExperiment
Liana Py
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99
LIANA+: an all-in-one framework for cell-cell communication
Infercnvpy
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97
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
Scatac Benchmarking
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92
Benchmarking computational single cell ATAC-seq methods
Mgatk
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89
mgatk: mitochondrial genome analysis toolkit
Sinto
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86
Tools for single-cell data processing
Moscot
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81
Multi-omic single-cell optimal transport tools
Cell_blast
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74
A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
Scnym
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71
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
Pertpy
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69
Perturbation Analysis in the scverse ecosystem.
Topometry
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69
Systematically learn and evaluate manifolds from high-dimensional data
Covid 19 Rna Seq Datasets
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61
A repository for sharing information on available COVID-19 RNA-Seq datasets
Scperturb
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56
scPerturb: A resource and a python/R tool for single-cell perturbation data
Scope
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56
Fast visualization tool for large-scale and high dimensional single-cell data
Scgnn
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53
scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks
Slat
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52
Spatial-Linked Alignment Tool
Cite Seq Count
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50
A tool that allows to get UMI counts from a single cell protein assay
Monopogen
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50
SNV calling from single cell sequencing
Cell2cell
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44
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
Cellhint
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44
A tool for semi-automatic cell type harmonization and integration
Nsforest
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40
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing
Cna
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38
Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
Cellsnp
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37
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
Scribe Py
⭐
36
Regulatory networks with Direct Information in python
Brie
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34
BRIE: Bayesian Regression for Isoform Estimate in Single Cells
Openproblems V2
⭐
31
Formalizing and benchmarking open problems in single-cell genomics
Schist
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30
An interface for Nested Stochastic Block Model for single cell analysis
Ngs
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30
Next-Gen Sequencing tools from the Horvath Lab
Cellar
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30
Interactive software tool for the assignment of cell types in single-cell studies.
Scnanogps
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29
Single cell Nanopore sequencing data for Genotype and Phenotype
Ot Scomics
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29
This Python package will allow you to replicate the experiments from our research on applying Optimal Transport as a similarity metric in between single-cell omics data.
Scalign
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28
A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches
Vitessce Python
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28
Python API and Jupyter widget for Vitessce
Split Seq_demultiplexing
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25
An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data
Scdino
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22
Self-Supervised Vision Transformers for multiplexed imaging datasets
Cell2sentence Ft
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21
Cell2Sentence turns scRNA-seq data into text for LLM training.
Dbmap
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20
A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.
Cshl Singlecell 2017
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20
Single Cell Analysis course at Cold Spring Harbor Laboratory 2017
Pyliger
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19
Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)
Crop Seq
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19
Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
Deepcycle
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19
Cell cycle inference in single-cell RNA-seq
Torch Adata
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17
Create PyTorch Datasets from AnnData
Spatialtis
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16
Spatial analysis toolkit for single cell multiplexed tissue data
Orange3 Single Cell
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16
🍊🔬 Orange add-on for gene expression of single cell data
Velodyn
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15
Dynamical systems methods for RNA velocity analysis
Maegatk
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14
Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
Lr Splitpipe
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13
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
Mdmcleaner
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13
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
Pysinglecellnet
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12
singleCellNet in Python
Gctree
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12
GCtree: phylogenetic inference of genotype-collapsed trees
Couplednmf
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11
Coupled clustering of single cell genomic data
Rna Combine
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11
RNA-seq data comprehensive data analysis toolbox
Ursm
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10
A Unified RNA Sequencing Model (URSM) for joint analysis of single cell and bulk RNA-seq data.
Scbean
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10
Single-cell data analysis
Proatac
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10
Preprocessing pipeline for (sc)ATAC data
Scmeta
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10
A python library for single-cell metabolism data analysis.
Scbs
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10
Python package with CLI for downstream analysis of single cell methylation data.
Transmorph
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10
Computational framework for dataset integration
Marcopolo
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9
MarcoPolo is a clustering-free approach to the exploration of bimodally expressed genes along with group information in single-cell RNA-seq data
Singlecell Qtl
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9
Discovery and characterization of variance QTLs in human induced pluripotent stem cells
Trisicell
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9
Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data
Cellcano
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8
Supervised cell type identification for scATAC-seq data
Cemba_data
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8
Mapping pipeline for snmC-seq based technologies.
Singlecellhaystack Py
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8
Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).
Irescue
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8
A tool to quantify transposable elements expression in scRNA-seq
Vega
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8
VEGA: VAE Enhanced by Gene Annotations
Scgv
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8
SCGV is an interactive graphical tool for single-cell genomics data, with emphasis on single-cell genomics of cancer
Discotoolkit_py
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7
DISCO by Scientist for Scientist for You
Scmmd
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7
Maximum mean discrepancy comparisons for single cell profiling experiments
Mudcod
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7
MuDCoD: Multi-subject Dynamic Community Detection
Archr H5ad
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7
Parse ArchR arrow files to anndata h5ad
Scphylo Tools
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5
a python toolkit for single-cell tumor phylogenetic analysis
Genomap
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5
Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
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