Research graph
References from Computational solutions for spatial transcriptomics. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/s41592-022-01409-2
10.1038/s41592-022-01409-2 · External reference
Spatially Resolved Transcriptomes-Next Generation Tools for Tissue Exploration
2020 · External reference
Spatially resolved, highly multiplexed RNA profiling in single cells
2015 · External reference
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10.1038/s41586-019-1049-y · External reference
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10.1038/nprot.2014.191 · External reference
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10.1038/s41587-020-0739-1 · External reference
10.1038/s41592-019-0548-y
10.1038/s41592-019-0548-y · External reference
Spatial multi-omics sequencing for fixed tissue via DBiT-seq
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10.1016/j.cell.2020.10.026
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10.1038/nmeth.2804 · External reference
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10.1038/s41592-020-0880-2 · External reference
10.1038/s41587-020-0472-9
10.1038/s41587-020-0472-9 · External reference
Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq
10.1038/nprot.2017.003 · 2017 · External reference
Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control
10.1038/s41467-018-06611-5 · 2018 · External reference
Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling
10.1038/ncomms12139 · 2016 · External reference
10.1093/nar/gkab120
10.1093/nar/gkab120 · External reference
Spatially resolved, highly multiplexed RNA profiling in single cells
2015 · External reference
Multiplexed detection of RNA using MERFISH and branched DNA amplification
2019 · External reference
10.1038/s41592-018-0175-z
10.1038/s41592-018-0175-z · External reference
10.1101/2021.11.03.467020
10.1101/2021.11.03.467020 · External reference
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10.1126/science.aaf2403 · External reference
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10.1101/2021.03.17.435795 · External reference
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10.1101/gr.275224.121
10.1101/gr.275224.121 · External reference
Spatial components of molecular tissue biology
2022 · External reference
Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects
2021 · External reference
Placing RNA in context and space – methods for spatially resolved transcriptomics
10.1111/febs.14435 · 2019 · External reference
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10.1038/s41586-020-03126-2 · External reference
10.1038/nmeth.2563
10.1038/nmeth.2563 · External reference
10.1016/j.cell.2018.05.035
10.1016/j.cell.2018.05.035 · External reference
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10.1073/pnas.1612826113 · External reference
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10.3389/fmolb.2021.768106 · 2022 · External reference
10.1038/nmeth.4500
10.1038/nmeth.4500 · External reference
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10.1038/nbt.4260 · External reference
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10.1038/s41592-018-0261-2 · 2019 · External reference
10.1371/journal.pcbi.1005177
10.1371/journal.pcbi.1005177 · External reference
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
2021 · External reference
10.1038/s41592-020-01018-x
10.1038/s41592-020-01018-x · External reference
10.1063/5.0027993
10.1063/5.0027993 · External reference
Cell segmentation-free inference of cell types from in situ transcriptomics data
2021 · External reference
10.1038/s41587-021-01044-w
10.1038/s41587-021-01044-w · External reference
Joint cell segmentation and cell type annotation for spatial transcriptomics
10.15252/msb.202010108 · 2021 · External reference
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10.21105/joss.02440 · External reference
10.5220/0008948000002513
10.5220/0008948000002513 · External reference
10.1261/rna.079073.121
10.1261/rna.079073.121 · External reference
EBImage-an R package for image processing with applications to cellular phenotypes
10.1093/bioinformatics/btq046 · 2010 · External reference
10.21105/joss.01012
10.21105/joss.01012 · External reference
10.1038/s41592-021-01358-2
10.1038/s41592-021-01358-2 · External reference
Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states
10.1073/pnas.2113568118 · 2021 · External reference
Unresolved reference
External reference
10.1101/2021.09.15.460240
10.1101/2021.09.15.460240 · External reference
10.1038/s41587-019-0392-8
10.1038/s41587-019-0392-8 · External reference
10.1126/science.aaw1219
10.1126/science.aaw1219 · External reference
10.1101/2021.10.21.465135
10.1101/2021.10.21.465135 · External reference
10.1101/2021.10.23.465550
10.1101/2021.10.23.465550 · External reference
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10.1016/j.devcel.2022.04.006 · External reference
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10.1016/j.devcel.2022.04.009 · External reference
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10.1016/j.celrep.2021.109915 · External reference
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10.1038/s41586-021-03852-1 · External reference
10.1038/s41588-021-00911-1
10.1038/s41588-021-00911-1 · External reference
10.1038/s41467-018-04724-5
10.1038/s41467-018-04724-5 · External reference
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
2020 · External reference
10.1101/2020.07.14.200600
10.1101/2020.07.14.200600 · External reference
10.1101/358937
10.1101/358937 · External reference
Spatial maps of hepatocellular carcinoma transcriptomes highlight an unexplored landscape of heterogeneity and a novel gene signature for survival
10.1186/s12935-021-02430-9 · 2022 · External reference
STAR: Ultrafast universal RNAseq aligner
10.1093/bioinformatics/bts635 · 2013 · External reference
10.1038/s41587-021-00870-2
10.1038/s41587-021-00870-2 · External reference
10.1093/bioinformatics/btx211
10.1093/bioinformatics/btx211 · External reference
10.1101/2021.05.05.442755
10.1101/2021.05.05.442755 · External reference
dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments
10.1186/s13059-018-1449-6 · 2018 · External reference
Analysis and Visualization of Spatial Transcriptomic Data
2022 · External reference
Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue
10.3389/fphys.2021.809346 · 2022 · External reference
10.1093/nar/gkab043
10.1093/nar/gkab043 · External reference
Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data
10.1038/s41467-022-28020-5 · 2022 · External reference
Cell 2location maps fine-grained cell types in spatial transcriptomics
10.1038/s41587-021-01139-4 · 2022 · External reference
10.1101/gr.275224.121
10.1101/gr.275224.121 · External reference
10.1038/nbt.4096
10.1038/nbt.4096 · External reference
Spatially informed cell-type deconvolution for spatial transcriptomics
10.1038/s41587-022-01273-7 · 2022 · External reference
Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data
10.1038/s41467-022-30033-z · 2022 · External reference
Best practices for spatial profiling for breast cancer research with the GeoMx(R) digital spatial profiler
10.3390/cancers13174456 · 2021 · External reference
10.1038/s41467-020-20139-7
10.1038/s41467-020-20139-7 · External reference
10.1038/s41467-021-27801-8
10.1038/s41467-021-27801-8 · External reference
10.1101/2021.09.29.462442
10.1101/2021.09.29.462442 · External reference
Inter- and intra-tumor heterogeneity of metastatic prostate cancer determined by digital spatial gene expression profiling
10.1038/s41467-021-21615-4 · 2021 · External reference
10.1002/1878-0261.13017
10.1002/1878-0261.13017 · External reference
Genome analysis identifies differences in the transcriptional targets of duodenal versus pancreatic neuroendocrine tumours
10.1136/bmjgast-2021-000765 · 2021 · External reference
Tumor Microenvironment Profiles Reveal Distinct Therapy-Oriented Proteogenomic Characteristics in Colorectal Cancer
2021 · External reference
10.1101/gr.265017.120
10.1101/gr.265017.120 · External reference
Statistical and machine learning methods for spatially resolved transcriptomics data analysis
10.1186/s13059-022-02653-7 · 2022 · External reference
Spatial molecular profiling: Platforms, applications and analysis tools
2021 · External reference
10.1016/j.cell.2021.04.048
10.1016/j.cell.2021.04.048 · External reference
Seamless integration of image and molecular analysis for spatial transcriptomics workflows
10.1186/s12864-020-06832-3 · 2020 · External reference
10.1101/2020.10.20.346544
10.1101/2020.10.20.346544 · External reference
A Python library for probabilistic analysis of single-cell omics data
10.1038/s41587-021-01206-w · 2022 · External reference
10.1101/2020.05.31.125658
10.1101/2020.05.31.125658 · External reference
Unresolved reference
External reference
10.1126/science.aad0501
10.1126/science.aad0501 · External reference
Current best practices in single-cell RNA-seq analysis: a tutorial
10.15252/msb.20188746 · 2019 · External reference
SCANPY: Large-scale single-cell gene expression data analysis
2018 · External reference
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
10.1186/s13059-019-1874-1 · 2019 · External reference
SCnorm: Robust normalization of single-cell RNA-seq data
10.1038/nmeth.4263 · 2017 · External reference
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
2016 · External reference
Optimization and expansion of non-negative matrix factorization
2020 · External reference
10.1038/s41587-021-00935-2
10.1038/s41587-021-00935-2 · External reference
10.1038/nmeth.4236
10.1038/nmeth.4236 · External reference
ILoReg: A tool for high-resolution cell population identification from single-cell RNA-seq data
10.1093/bioinformatics/btaa919 · 2021 · External reference
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10.1038/nmeth.4207 · External reference
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10.1038/s41587-021-01001-7 · External reference
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10.1038/s41590-018-0276-y · External reference
10.1093/nar/gkz543
10.1093/nar/gkz543 · External reference
10.1101/2021.11.08.467740
10.1101/2021.11.08.467740 · External reference
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10.1016/j.isci.2020.101913 · External reference
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10.1093/bioinformatics/btz914 · External reference
10.1038/nmeth.4463
10.1038/nmeth.4463 · External reference
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10.1038/s41596-020-0336-2 · External reference
RNA velocity–current challenges and future perspectives
10.15252/msb.202110282 · 2021 · External reference
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10.1038/nmeth.4636 · External reference
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10.1038/s41592-019-0701-7 · External reference
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10.1038/nmeth.4634 · External reference
10.1101/2021.10.27.466045
10.1101/2021.10.27.466045 · External reference
10.1101/gr.271288.120
10.1101/gr.271288.120 · External reference
10.1016/j.cels.2021.04.005
10.1016/j.cels.2021.04.005 · External reference
10.1038/nbt.4260
10.1038/nbt.4260 · External reference
Deep Learning of Histopathology Images at the Single Cell Level
2021 · External reference
10.1038/s41592-021-01255-8
10.1038/s41592-021-01255-8 · External reference
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10.1038/s41592-019-0667-5 · External reference
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2021 · External reference
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10.1186/s13059-022-02663-5 · External reference
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