These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
42. Robust decomposition of cell type mixtures in spatial transcriptomics. Cable DM; Murray E; Zou LS; Goeva A; Macosko EZ; Chen F; Irizarry RA Nat Biotechnol; 2022 Apr; 40(4):517-526. PubMed ID: 33603203 [TBL] [Abstract][Full Text] [Related]
43. DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data. Karikomi M; Zhou P; Nie Q Brief Bioinform; 2022 Jul; 23(4):. PubMed ID: 35709795 [TBL] [Abstract][Full Text] [Related]
44. SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression. Liu Y; Wang T; Duggan B; Sharpnack M; Huang K; Zhang J; Ye X; Johnson TS Brief Bioinform; 2022 May; 23(3):. PubMed ID: 35380614 [TBL] [Abstract][Full Text] [Related]
45. Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes. Cobos FA; Panah MJN; Epps J; Long X; Man TK; Chiu HS; Chomsky E; Kiner E; Krueger MJ; di Bernardo D; Voloch L; Molenaar J; van Hooff SR; Westermann F; Jansky S; Redell ML; Mestdagh P; Sumazin P Genome Biol; 2023 Aug; 24(1):177. PubMed ID: 37528411 [TBL] [Abstract][Full Text] [Related]
46. Computational Analysis of Single-Cell RNA-Seq Data. Alessandrì L; Cordero F; Beccuti M; Arigoni M; Calogero RA Methods Mol Biol; 2021; 2284():289-301. PubMed ID: 33835449 [TBL] [Abstract][Full Text] [Related]
47. New generative methods for single-cell transcriptome data in bulk RNA sequence deconvolution. Nishikawa T; Lee M; Amau M Sci Rep; 2024 Feb; 14(1):4156. PubMed ID: 38378978 [TBL] [Abstract][Full Text] [Related]
48. Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data. Stock M; Popp N; Fiorentino J; Scialdone A Bioinformatics; 2024 May; 40(5):. PubMed ID: 38627250 [TBL] [Abstract][Full Text] [Related]
49. ST Pipeline: an automated pipeline for spatial mapping of unique transcripts. Navarro JF; Sjöstrand J; Salmén F; Lundeberg J; Ståhl PL Bioinformatics; 2017 Aug; 33(16):2591-2593. PubMed ID: 28398467 [TBL] [Abstract][Full Text] [Related]
50. Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments. Tian L; Dong X; Freytag S; Lê Cao KA; Su S; JalalAbadi A; Amann-Zalcenstein D; Weber TS; Seidi A; Jabbari JS; Naik SH; Ritchie ME Nat Methods; 2019 Jun; 16(6):479-487. PubMed ID: 31133762 [TBL] [Abstract][Full Text] [Related]
52. Single-cell and spatial transcriptomics approaches of cardiovascular development and disease. Roth R; Kim S; Kim J; Rhee S BMB Rep; 2020 Aug; 53(8):393-399. PubMed ID: 32684243 [TBL] [Abstract][Full Text] [Related]
53. EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning. Tu JJ; Li HS; Yan H; Zhang XF Bioinformatics; 2023 Jan; 39(1):. PubMed ID: 36610709 [TBL] [Abstract][Full Text] [Related]
54. Normalization of Single-Cell RNA-Seq Data. Risso D Methods Mol Biol; 2021; 2284():303-329. PubMed ID: 33835450 [TBL] [Abstract][Full Text] [Related]
55. NNICE: a deep quantile neural network algorithm for expression deconvolution. Jin YW; Hu P; Liu Q Sci Rep; 2024 Jun; 14(1):14040. PubMed ID: 38890415 [TBL] [Abstract][Full Text] [Related]
56. A systematic evaluation of state-of-the-art deconvolution methods in spatial transcriptomics: insights from cardiovascular disease and chronic kidney disease. Slabowska AO; Pyke C; Hvid H; Jessen LE; Baumgart S; Das V Front Bioinform; 2024; 4():1352594. PubMed ID: 38601476 [TBL] [Abstract][Full Text] [Related]
57. A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data. Ospina O; Soupir A; Fridley BL Methods Mol Biol; 2023; 2629():115-140. PubMed ID: 36929076 [TBL] [Abstract][Full Text] [Related]
58. Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data. Miller BF; Huang F; Atta L; Sahoo A; Fan J Nat Commun; 2022 Apr; 13(1):2339. PubMed ID: 35487922 [TBL] [Abstract][Full Text] [Related]
59. Benchmarking cell-type clustering methods for spatially resolved transcriptomics data. Cheng A; Hu G; Li WV Brief Bioinform; 2023 Jan; 24(1):. PubMed ID: 36410733 [TBL] [Abstract][Full Text] [Related]
60. Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. Nadel BB; Oliva M; Shou BL; Mitchell K; Ma F; Montoya DJ; Mouton A; Kim-Hellmuth S; Stranger BE; Pellegrini M; Mangul S Brief Bioinform; 2021 Nov; 22(6):. PubMed ID: 34346485 [TBL] [Abstract][Full Text] [Related] [Previous] [Next] [New Search]