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The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature biotechnology, 2023-05, Vol.41 (5), p.604-606

2023

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Banach Space Theory: The Basis for Linear and Nonlinear Analysis

1, 2011

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Current best practices in single‐cell RNA‐seq analysis: a tutorial

Molecular systems biology, 2019-06, Vol.15 (6), p.e8746-n/a

2019

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Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

PLoS computational biology, 2017-01, Vol.13 (1), p.e1005331-e1005331

2017

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SCANPY: large-scale single-cell gene expression data analysis

Genome Biology, 2018-02, Vol.19 (1), p.15-15, Article 15

2018

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Diffusion maps for high-dimensional single-cell analysis of differentiation data

Bioinformatics, 2015-09, Vol.31 (18), p.2989-2998

2015

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Generalizing RNA velocity to transient cell states through dynamical modeling

Nature biotechnology, 2020-12, Vol.38 (12), p.1408-1414

2020

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Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

Genome Biology, 2021-10, Vol.22 (1), p.301-301, Article 301

2021

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Single-cell RNA-seq denoising using a deep count autoencoder

Nature communications, 2019-01, Vol.10 (1), p.390-390, Article 390

2019

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A test metric for assessing single-cell RNA-seq batch correction

Nature methods, 2019-01, Vol.16 (1), p.43

2019

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Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

Molecular systems biology, 2022-03, Vol.18 (3), p.e10798-n/a

2022

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destiny: diffusion maps for large-scale single-cell data in R

Bioinformatics, 2016-04, Vol.32 (8), p.1241-1243

2016

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Diffusion pseudotime robustly reconstructs lineage branching

Nature methods, 2016-10, Vol.13 (10), p.845

2016

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Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion

PLoS computational biology, 2016-07, Vol.12 (7), p.e1005030-e1005030

2016

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Spatial components of molecular tissue biology

Nature biotechnology, 2022-03, Vol.40 (3), p.308-318

2022

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Deep learning: new computational modelling techniques for genomics

Nature reviews. Genetics, 2019-07, Vol.20 (7), p.389

2019

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PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

Genome Biology, 2019-03, Vol.20 (1), p.59-9, Article 59

2019

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Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network

PloS one, 2011-08, Vol.6 (8), p.e22649-e22649

2011

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Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

Cell stem cell, 2015-06, Vol.16 (6), p.712-724

2015

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CellRank for directed single-cell fate mapping

Nature methods, 2022-02, Vol.19 (2), p.159

2022

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Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Nature biotechnology, 2015-02, Vol.33 (2), p.155-160

2015

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Squidpy: a scalable framework for spatial omics analysis

Nature methods, 2022-02, Vol.19 (2), p.171

2022

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A BaSiC tool for background and shading correction of optical microscopy images

Nature communications, 2017-06, Vol.8 (1), p.14836-14836, Article 14836

2017

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RNA velocity—current challenges and future perspectives

Molecular systems biology, 2021-08, Vol.17 (8), p.e10282-n/a

2021

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Benchmarking atlas-level data integration in single-cell genomics

Nature methods, 2022-01, Vol.19 (1), p.41

2022

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The scverse project provides a computational ecosystem for single-cell omics data analysis

Banach Space Theory: The Basis for Linear and Nonlinear Analysis

Current best practices in single‐cell RNA‐seq analysis: a tutorial

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

SCANPY: large-scale single-cell gene expression data analysis

Diffusion maps for high-dimensional single-cell analysis of differentiation data

Generalizing RNA velocity to transient cell states through dynamical modeling

Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

Single-cell RNA-seq denoising using a deep count autoencoder

A test metric for assessing single-cell RNA-seq batch correction

Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

destiny: diffusion maps for large-scale single-cell data in R

Diffusion pseudotime robustly reconstructs lineage branching

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion

Spatial components of molecular tissue biology

Deep learning: new computational modelling techniques for genomics

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

CellRank for directed single-cell fate mapping

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Squidpy: a scalable framework for spatial omics analysis

A BaSiC tool for background and shading correction of optical microscopy images

RNA velocity—current challenges and future perspectives

Benchmarking atlas-level data integration in single-cell genomics

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