메뉴 건너뛰기




Volumn 591, Issue 15, 2017, Pages 2213-2225

Computational approaches for interpreting scRNA-seq data

Author keywords

single cell analysis methods and tools; single cell genomics

Indexed keywords

BAYES THEOREM; CELL HETEROGENEITY; CELLULAR DISTRIBUTION; GENE EXPRESSION; GENE REGULATORY NETWORK; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; HUMAN; LYMPHOCYTE DIFFERENTIATION; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA SEQUENCE; SINGLE CELL ANALYSIS; T LYMPHOCYTE; TFH CELL; TH1 CELL; TRANSCRIPTOMICS; WHOLE GENOME SEQUENCING; ANIMAL; BIOLOGY; CLUSTER ANALYSIS; PROCEDURES; SEQUENCE ANALYSIS;

EID: 85021301728     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1002/1873-3468.12684     Document Type: Review
Times cited : (96)

References (89)
  • 3
    • 85010878111 scopus 로고    scopus 로고
    • Single-cell mRNA quantification and differential analysis with Census
    • Qiu X, Hill A, Packer J, Lin D, Ma Y-A and Trapnell C (2017) Single-cell mRNA quantification and differential analysis with Census. Nat Methods 14, 309–315.
    • (2017) Nat Methods , vol.14 , pp. 309-315
    • Qiu, X.1    Hill, A.2    Packer, J.3    Lin, D.4    Ma, Y.-A.5    Trapnell, C.6
  • 4
    • 84962684884 scopus 로고    scopus 로고
    • Robust detection of alternative splicing in a population of single cells
    • Welch JD, Hu Y and Prins JF (2016) Robust detection of alternative splicing in a population of single cells. Nucleic Acids Res 44, e73.
    • (2016) Nucleic Acids Res , vol.44
    • Welch, J.D.1    Hu, Y.2    Prins, J.F.3
  • 6
    • 84892179132 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
    • Deng Q, Ramsköld D, Reinius B and Sandberg R (2014) Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343, 193–196.
    • (2014) Science , vol.343 , pp. 193-196
    • Deng, Q.1    Ramsköld, D.2    Reinius, B.3    Sandberg, R.4
  • 7
    • 84944901262 scopus 로고    scopus 로고
    • Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression
    • Kim JK, Kolodziejczyk AA, Ilicic T, Illicic T, Teichmann SA and Marioni JC (2015) Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. Nat Commun 6, 8687.
    • (2015) Nat Commun , vol.6 , pp. 8687
    • Kim, J.K.1    Kolodziejczyk, A.A.2    Ilicic, T.3    Illicic, T.4    Teichmann, S.A.5    Marioni, J.C.6
  • 9
    • 84954396263 scopus 로고    scopus 로고
    • Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data
    • Kim JK and Marioni JC (2013) Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data. Genome Biol 14, R7.
    • (2013) Genome Biol , vol.14 , pp. R7
    • Kim, J.K.1    Marioni, J.C.2
  • 10
    • 85027437879 scopus 로고    scopus 로고
    • Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression
    • Kar G, Kim JK, Kolodziejczyk AA and Natarajan KN (2017) Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression. bioRxiv, https://doi.org/10.1101/117267
    • (2017) bioRxiv
    • Kar, G.1    Kim, J.K.2    Kolodziejczyk, A.A.3    Natarajan, K.N.4
  • 21
    • 84923647450 scopus 로고    scopus 로고
    • Computational and analytical challenges in single-cell transcriptomics
    • Stegle O, Teichmann SA and Marioni JC (2015) Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet 16, 133–145.
    • (2015) Nat Rev Genet , vol.16 , pp. 133-145
    • Stegle, O.1    Teichmann, S.A.2    Marioni, J.C.3
  • 23
    • 85003441754 scopus 로고    scopus 로고
    • Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation
    • Love MI, Hogenesch JB and Irizarry RA (2016) Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nat Biotechnol 34, 1287–1291.
    • (2016) Nat Biotechnol , vol.34 , pp. 1287-1291
    • Love, M.I.1    Hogenesch, J.B.2    Irizarry, R.A.3
  • 26
    • 84883492771 scopus 로고    scopus 로고
    • Kraken: a set of tools for quality control and analysis of high-throughput sequence data
    • Davis MPA, van Dongen S, Abreu-Goodger C, Bartonicek N and Enright AJ (2013) Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods 63, 41–49.
    • (2013) Methods , vol.63 , pp. 41-49
    • Davis, M.P.A.1    van Dongen, S.2    Abreu-Goodger, C.3    Bartonicek, N.4    Enright, A.J.5
  • 27
    • 85010007467 scopus 로고    scopus 로고
    • scater: Pre-processing, quality control, normalisation and visualisation of single-cell RNA-seq data in R
    • McCarthy DJ, Campbell KR, Lun ATL and Wills QF (2016) scater: Pre-processing, quality control, normalisation and visualisation of single-cell RNA-seq data in R. bioRxiv, https://doi.org/10.1101/069633
    • (2016) bioRxiv
    • McCarthy, D.J.1    Campbell, K.R.2    Lun, A.T.L.3    Wills, Q.F.4
  • 30
    • 84946226911 scopus 로고    scopus 로고
    • Design and analysis of single-cell sequencing experiments
    • Grün D and van Oudenaarden A (2015) Design and analysis of single-cell sequencing experiments. Cell 163, 799–810.
    • (2015) Cell , vol.163 , pp. 799-810
    • Grün, D.1    van Oudenaarden, A.2
  • 31
    • 0000325341 scopus 로고
    • LIII. On lines and planes of closest fit to systems of points in space
    • Pearson K (1901) LIII. On lines and planes of closest fit to systems of points in space. Philos Mag Series 6 2, 559–572.
    • (1901) Philos Mag Series 6 , vol.2 , pp. 559-572
    • Pearson, K.1
  • 33
    • 84955706109 scopus 로고    scopus 로고
    • ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis
    • Pierson E and Yau C (2015) ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis. Genome Biol 16, 241.
    • (2015) Genome Biol , vol.16 , pp. 241
    • Pierson, E.1    Yau, C.2
  • 35
    • 84931072284 scopus 로고    scopus 로고
    • Identification of cell types from single-cell transcriptomes using a novel clustering method
    • Xu C and Su Z (2015) Identification of cell types from single-cell transcriptomes using a novel clustering method. Bioinformatics 31, 1974–1980.
    • (2015) Bioinformatics , vol.31 , pp. 1974-1980
    • Xu, C.1    Su, Z.2
  • 37
    • 85014528252 scopus 로고    scopus 로고
    • Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning
    • Wang B, Zhu J, Pierson E, Ramazzotti D and Batzoglou S (2017) Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. Nat Methods 14, 414–416.
    • (2017) Nat Methods , vol.14 , pp. 414-416
    • Wang, B.1    Zhu, J.2    Pierson, E.3    Ramazzotti, D.4    Batzoglou, S.5
  • 38
    • 33746476985 scopus 로고    scopus 로고
    • Diffusion maps and coarse-graining: a unified framework for dimensionality reduction, graph partitioning, and data set parameterization
    • Lafon S and Lee AB (2006) Diffusion maps and coarse-graining: a unified framework for dimensionality reduction, graph partitioning, and data set parameterization. IEEE Trans Pattern Anal Mach Intell 28, 1393–1403.
    • (2006) IEEE Trans Pattern Anal Mach Intell , vol.28 , pp. 1393-1403
    • Lafon, S.1    Lee, A.B.2
  • 39
    • 84944178665 scopus 로고
    • Hierarchical grouping to optimize an objective function
    • Ward JH Jr (1963) Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58, 236–244.
    • (1963) J Am Stat Assoc , vol.58 , pp. 236-244
    • Ward, J.H.1
  • 40
    • 0041965980 scopus 로고    scopus 로고
    • Cluster ensembles—a knowledge reuse framework for combining multiple partitions
    • Strehl A and Ghosh J (2002) Cluster ensembles—a knowledge reuse framework for combining multiple partitions. J Mach Learn Res 3, 583–617.
    • (2002) J Mach Learn Res , vol.3 , pp. 583-617
    • Strehl, A.1    Ghosh, J.2
  • 42
    • 0037620665 scopus 로고    scopus 로고
    • Reconstructing the temporal ordering of biological samples using microarray data
    • Magwene PM, Lizardi P and Kim J (2003) Reconstructing the temporal ordering of biological samples using microarray data. Bioinformatics 19, 842–850.
    • (2003) Bioinformatics , vol.19 , pp. 842-850
    • Magwene, P.M.1    Lizardi, P.2    Kim, J.3
  • 43
    • 85027436429 scopus 로고    scopus 로고
    • Reversed graph embedding resolves complex single-cell developmental trajectories
    • Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner H and Trapnell C (2017) Reversed graph embedding resolves complex single-cell developmental trajectories. bioRxiv, https://doi.org/10.1101/110668
    • (2017) bioRxiv
    • Qiu, X.1    Mao, Q.2    Tang, Y.3    Wang, L.4    Chawla, R.5    Pliner, H.6    Trapnell, C.7
  • 46
    • 84999791835 scopus 로고    scopus 로고
    • Order under uncertainty: robust differential expression analysis using probabilistic models for pseudotime inference
    • Campbell KR and Yau C (2016) Order under uncertainty: robust differential expression analysis using probabilistic models for pseudotime inference. PLoS Comput Biol 12, e1005212.
    • (2016) PLoS Comput Biol , vol.12
    • Campbell, K.R.1    Yau, C.2
  • 48
    • 85021263276 scopus 로고    scopus 로고
    • Ouija: Incorporating prior knowledge in single-cell trajectory learning using Bayesian nonlinear factor analysis
    • Campbell K and Yau C (2016) Ouija: Incorporating prior knowledge in single-cell trajectory learning using Bayesian nonlinear factor analysis. bioRxiv.
    • (2016) bioRxiv
    • Campbell, K.1    Yau, C.2
  • 51
    • 84977080410 scopus 로고    scopus 로고
    • Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development
    • Chen J, Schlitzer A, Chakarov S, Ginhoux F and Poidinger M (2016) Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development. Nat Commun 7, 11988.
    • (2016) Nat Commun , vol.7 , pp. 11988
    • Chen, J.1    Schlitzer, A.2    Chakarov, S.3    Ginhoux, F.4    Poidinger, M.5
  • 52
    • 0001745298 scopus 로고
    • The interpretation of interaction in contingency tables
    • Simpson EH (1951) The interpretation of interaction in contingency tables. J R Stat Soc Series B Stat Methodol 13, 238–241.
    • (1951) J R Stat Soc Series B Stat Methodol , vol.13 , pp. 238-241
    • Simpson, E.H.1
  • 53
    • 0001308326 scopus 로고
    • Notes on the theory of association of attributes in statistics
    • Yule GU (1903) Notes on the theory of association of attributes in statistics. Biometrika 2, 121–134.
    • (1903) Biometrika , vol.2 , pp. 121-134
    • Yule, G.U.1
  • 54
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson WE, Li C and Rabinovic A (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118–127.
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 56
    • 84909644283 scopus 로고    scopus 로고
    • Normalization of RNA-seq data using factor analysis of control genes or samples
    • Risso D, Ngai J, Speed TP and Dudoit S (2014) Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol 32, 896–902.
    • (2014) Nat Biotechnol , vol.32 , pp. 896-902
    • Risso, D.1    Ngai, J.2    Speed, T.P.3    Dudoit, S.4
  • 57
    • 84859098571 scopus 로고    scopus 로고
    • The sva package for removing batch effects and other unwanted variation in high-throughput experiments
    • Leek JT, Johnson WE, Parker HS, Jaffe AE and Storey JD (2012) The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28, 882–883.
    • (2012) Bioinformatics , vol.28 , pp. 882-883
    • Leek, J.T.1    Johnson, W.E.2    Parker, H.S.3    Jaffe, A.E.4    Storey, J.D.5
  • 58
    • 84925226706 scopus 로고    scopus 로고
    • svaseq: Removing batch effects and other unwanted noise from sequencing data
    • Leek JT (2014) svaseq: Removing batch effects and other unwanted noise from sequencing data. Nucleic Acids Res, https://doi:10.1093/nar/gku864
    • (2014) Nucleic Acids Res
    • Leek, J.T.1
  • 59
    • 84861734626 scopus 로고    scopus 로고
    • Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
    • Stegle O, Parts L, Piipari M, Winn J and Durbin R (2012) Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat Protoc 7, 500–507.
    • (2012) Nat Protoc , vol.7 , pp. 500-507
    • Stegle, O.1    Parts, L.2    Piipari, M.3    Winn, J.4    Durbin, R.5
  • 60
    • 84901831004 scopus 로고    scopus 로고
    • Validation of noise models for single-cell transcriptomics
    • Grün D, Kester L and van Oudenaarden A (2014) Validation of noise models for single-cell transcriptomics. Nat Methods 11, 637–640.
    • (2014) Nat Methods , vol.11 , pp. 637-640
    • Grün, D.1    Kester, L.2    van Oudenaarden, A.3
  • 64
    • 84924629414 scopus 로고    scopus 로고
    • Differential analysis of count data–the DESeq2 package
    • Love M, Anders S and Huber W (2014) Differential analysis of count data–the DESeq2 package. Genome Biol 15, 550.
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.1    Anders, S.2    Huber, W.3
  • 65
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ and Smyth GK (2010) edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 66
  • 67
    • 85029221521 scopus 로고    scopus 로고
    • Modelling dropouts allows for unbiased identification of marker genes in scRNASeq experiments
    • Andrews TS and Hemberg M (2016) Modelling dropouts allows for unbiased identification of marker genes in scRNASeq experiments. bioRxiv.
    • (2016) bioRxiv
    • Andrews, T.S.1    Hemberg, M.2
  • 68
    • 84903574951 scopus 로고    scopus 로고
    • Bayesian approach to single-cell differential expression analysis
    • Kharchenko PV, Silberstein L and Scadden DT (2014) Bayesian approach to single-cell differential expression analysis. Nat Methods 11, 740–742.
    • (2014) Nat Methods , vol.11 , pp. 740-742
    • Kharchenko, P.V.1    Silberstein, L.2    Scadden, D.T.3
  • 71
    • 79956211692 scopus 로고    scopus 로고
    • A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression
    • Kalaitzis AA and Lawrence ND (2011) A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression. BMC Bioinformat 12, 180.
    • (2011) BMC Bioinformat , vol.12 , pp. 180
    • Kalaitzis, A.A.1    Lawrence, N.D.2
  • 72
    • 85019119633 scopus 로고    scopus 로고
    • switchde: Inference of switch-like differential expression along single-cell trajectories
    • Campbell KR and Yau C (2017) switchde: Inference of switch-like differential expression along single-cell trajectories. Bioinformatics 33, 1241–1242.
    • (2017) Bioinformatics , vol.33 , pp. 1241-1242
    • Campbell, K.R.1    Yau, C.2
  • 73
    • 85020058202 scopus 로고    scopus 로고
    • ImpulseDE: Detection of differentially expressed genes in time series data using impulse models
    • Sander J, Schultze JL and Yosef N (2017) ImpulseDE: Detection of differentially expressed genes in time series data using impulse models. Bioinformatics 33, 757–759.
    • (2017) Bioinformatics , vol.33 , pp. 757-759
    • Sander, J.1    Schultze, J.L.2    Yosef, N.3
  • 75
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • Langfelder P and Horvath S (2008) WGCNA: An R package for weighted correlation network analysis. BMC Bioinformat 9, 559.
    • (2008) BMC Bioinformat , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 77
    • 84962711132 scopus 로고    scopus 로고
    • OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data
    • Leng N, Choi J, Chu L-F, Thomson JA, Kendziorski C and Stewart R (2016) OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data. Bioinformatics 32, 1408–1410.
    • (2016) Bioinformatics , vol.32 , pp. 1408-1410
    • Leng, N.1    Choi, J.2    Chu, L.-F.3    Thomson, J.A.4    Kendziorski, C.5    Stewart, R.6
  • 82
    • 84934441202 scopus 로고    scopus 로고
    • Single-neuron transcriptome and methylome sequencing for epigenomic analysis of aging
    • Moroz LL and Kohn AB (2013) Single-neuron transcriptome and methylome sequencing for epigenomic analysis of aging. Methods Mol Biol 1048, 323–352.
    • (2013) Methods Mol Biol , vol.1048 , pp. 323-352
    • Moroz, L.L.1    Kohn, A.B.2
  • 84
    • 77956412152 scopus 로고    scopus 로고
    • Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis
    • Tang F, Barbacioru C, Bao S, Lee C, Nordman E, Wang X, Lao K and Surani MA (2010) Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell 6, 468–478.
    • (2010) Cell Stem Cell , vol.6 , pp. 468-478
    • Tang, F.1    Barbacioru, C.2    Bao, S.3    Lee, C.4    Nordman, E.5    Wang, X.6    Lao, K.7    Surani, M.A.8
  • 86
    • 84956681316 scopus 로고    scopus 로고
    • Single-cell technologies to study the immune system
    • Proserpio V and Mahata B (2016) Single-cell technologies to study the immune system. Immunology 147, 133–140.
    • (2016) Immunology , vol.147 , pp. 133-140
    • Proserpio, V.1    Mahata, B.2
  • 87
    • 84994065736 scopus 로고    scopus 로고
    • Genetics and immunity in the era of single-cell genomics
    • Vieira Braga FA, Teichmann SA and Chen X (2016) Genetics and immunity in the era of single-cell genomics. Hum Mol Genet 25, R141–R148.
    • (2016) Hum Mol Genet , vol.25 , pp. R141-R148
    • Vieira Braga, F.A.1    Teichmann, S.A.2    Chen, X.3
  • 88
    • 84942917849 scopus 로고    scopus 로고
    • The first five years of single-cell cancer genomics and beyond
    • Navin NE (2015) The first five years of single-cell cancer genomics and beyond. Genome Res 25, 1499–1507.
    • (2015) Genome Res , vol.25 , pp. 1499-1507
    • Navin, N.E.1
  • 89
    • 84997189950 scopus 로고    scopus 로고
    • Cancer genomics: single-cell RNA-seq to decipher tumour architecture
    • Cloney R (2017) Cancer genomics: single-cell RNA-seq to decipher tumour architecture. Nat Rev Genet 18, 2–3.
    • (2017) Nat Rev Genet , vol.18 , pp. 2-3
    • Cloney, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.