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Comparison of clustering methods for high‐dimensional single‐cell flow and mass cytometry data

Cytometry. Part A, 2016-12, Vol.89 (12), p.1084-1096

2016

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High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

Nature medicine, 2018-02, Vol.24 (2), p.144-153

2018

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Essential guidelines for computational method benchmarking

Genome Biology, 2019-06, Vol.20 (1), p.125-125, Article 125

2019

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miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

PLoS computational biology, 2021-08, Vol.17 (8), p.e1009290-e1009290

2021

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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

BMC genomics, 2022-06, Vol.23 (1), p.434-434, Article 434

2022

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nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes

Nature communications, 2023-07, Vol.14 (1), p.4059-4059, Article 4059

2023

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CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets [version 2; peer review: 2 approved]

F1000 research, 2017, Vol.6, p.748

2017

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High-dimensional single-cell analysis reveals the immune signature of narcolepsy

The Journal of experimental medicine, 2016-11, Vol.213 (12), p.2621-2633

2016

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diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

Communications biology, 2019-05, Vol.2 (1), p.183-183, Article 183

2019

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Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors

Genome Biology, 2023-10, Vol.24 (1), p.239-239, Article 239

2023

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Statistical methods for detecting differentially methylated loci and regions

Frontiers in genetics, 2014-09, Vol.5, p.324-324

2014

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The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

eLife, 2024-01, Vol.12

2024

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Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

Gigascience, 2021-09, Vol.10 (9)

2021

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HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats [version 2; peer review: 2 approved]

F1000 research, 2019, Vol.8, p.1459-1459

2019

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Complement downregulation promotes an inflammatory signature that renders colorectal cancer susceptible to immunotherapy

Journal for immunotherapy of cancer, 2022-09, Vol.10 (9), p.e004717

2022

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Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Nature neuroscience, 2021-03, Vol.24 (3), p.425-436

2021

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Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes

Development (Cambridge), 2016-06, Vol.143 (11), p.2025-2037

2016

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An updated guide for the perplexed: cytometry in the high-dimensional era

Nature immunology, 2021-10, Vol.22 (10), p.1190-1197

2021

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SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

Bioinformatics, 2022-05, Vol.38 (11), p.3128-3131

2022

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VistoSeg : Processing utilities for high-resolution images for spatially resolved transcriptomics data

Biological imaging (Cambridge, England), 2023, Vol.3, p.e23, Article e23

2023

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Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis

The FASEB journal, 2020-03, Vol.34 (3), p.4204-4218

2020

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CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets [version 4; peer review: 2 approved]

F1000 research, 2019-12, Vol.6, p.748

2019

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CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets [version 3; peer review: 2 approved]

F1000 research, 2019-05, Vol.6, p.748-748

2019

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CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

F1000 research, 2017, Vol.6, p.748

2017

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HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats [version 1; peer review: 2 approved with reservations]

F1000 research, 2019, Vol.8, p.1459

2019

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Comparison of clustering methods for high‐dimensional single‐cell flow and mass cytometry data

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

Essential guidelines for computational method benchmarking

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets [version 2; peer review: 2 approved]

High-dimensional single-cell analysis reveals the immune signature of narcolepsy

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors

Statistical methods for detecting differentially methylated loci and regions

The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats [version 2; peer review: 2 approved]

Complement downregulation promotes an inflammatory signature that renders colorectal cancer susceptible to immunotherapy

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes

An updated guide for the perplexed: cytometry in the high-dimensional era

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

VistoSeg : Processing utilities for high-resolution images for spatially resolved transcriptomics data

Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets [version 4; peer review: 2 approved]

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets [version 3; peer review: 2 approved]

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats [version 1; peer review: 2 approved with reservations]

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