Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: tsne
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/tsne
T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
4 versions
Latest release: almost 3 years ago
7 dependent packages
1,974 downloads last month
Papers Mentioning tsne 26
10.3389/fgene.2021.667936
Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During InfectionsCited by: 9
Author(s): Matineh Rahmatbakhsh, Alla Gagarinova, Mohan Babu
Software Mentions: 21
Published: over 3 years ago
10.1186/s12920-019-0578-4
Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patientsCited by: 21
Author(s): Petr V. Nazarov, Anke Wienecke-Baldacchino, Andreï Zinovyev, Urszula Czerwińska, Arnaud Muller, Dorothée Nashan, Gunnar Dittmar, Francisco Azuaje, Stephanie Kreis
Software Mentions: 14
Published: over 5 years ago
10.1038/s42003-019-0554-8
Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcomeCited by: 37
Author(s): Weiyan Chen, Samuel Morabito, Kai Kessenbrock, Tariq Enver, Kerstin B. Meyer, Andrew E. Teschendorff
Software Mentions: 14
Published: over 5 years ago
10.4049/immunohorizons.1900097
Mass Cytometry Defines Virus-Specific CD4+ T Cells in Influenza VaccinationCited by: 3
Author(s): Priyanka B. Subrahmanyam, Tyson H. Holmes, Derek Lin, Laura F. Su, Gerlinde Obermoser, Jacques Banchereau, Virginia Pascual, Adolfo Garcı́a-Sastre, Randy A. Albrecht, Karolina Palucka, Mark M. Davis, Holden T. Maecker
Software Mentions: 13
Published: about 4 years ago
10.1111/jcmm.15939
Prognostic value and immune cell infiltration of hypoxic phenotype‐related gene signatures in glioblastoma microenvironmentCited by: 10
Author(s): Kai Xiao, Jun Tan, Jian Yuan, Gang Peng, Wenyong Long, Jun Su, Yao Xiao, Qian Xiao, Changwu Wu, Chaoying Qin, Lili Hu, Kaili Liu, Shunlian Liu, Hao Zhou, Yichong Ning, Xiaojuan Ding, Qing Liu
Software Mentions: 11
Published: about 4 years ago
10.3389/fimmu.2018.02191
Single Cell RNA Sequencing Identifies HSPG2 and APLNR as Markers of Endothelial Cell Injury in Systemic Sclerosis SkinCited by: 48
Author(s): Sokratis A. Apostolidis, Giuseppina Stifano, Tracy Tabib, Lisa Rice, Christina Morse, Bashar Kahaleh, Robert Lafyatis
Software Mentions: 11
Published: about 6 years ago
10.1371/journal.pone.0158259
Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast CancersCited by: 15
Author(s): Inna Tishchenko, Heloisa Helena Milioli, Carlos Riveros, Pablo Moscato
Software Mentions: 9
Published: over 8 years ago
10.1371/journal.pcbi.1006076
Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics dataCited by: 211
Author(s): Travers Ching, Xun Zhu, Lana X. Garmire
Software Mentions: 8
Published: over 6 years ago
10.1038/s41598-021-96160-7
Wolves, dogs and humans in regular contact can mutually impact each other’s skin microbiotaCited by: 6
Author(s): Stefanie U. Wetzels, Cameron Strachan, Beate Conrady, Martin Wagner, Iwan Burgener, Zsófia Virányi, Evelyne Selberherr
Software Mentions: 8
Published: over 3 years ago
10.1093/g3journal/jkaa036
Visualizing population structure with variational autoencodersCited by: 44
Author(s): C. J. Battey, Gabrielle C. Coffing, Andrew D. Kern
Software Mentions: 7
Published: almost 4 years ago
10.1186/s13073-019-0657-3
A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseasesCited by: 67
Author(s): Danuta R. Gawel, Jordi Serra-Musach, Sandra Lilja, Jesper Aagesen, Àlex Arenas, B. Asking, Malin Bengnér, Janne Björkander, Sophie Biggs, Jan Ernerudh, Henrik Hjortswang, Jan‐Erik Karlsson, Mattias Köpsén, Eun Jung Lee, Antonio Lentini, Xinxiu Li, Mattias Magnusson, David Martínez-Enguita, Andreas Matussek, Colm E. Nestor, Samuel Schäfer, Oliver Seifert, Ceylan Sonmez, Henrik Stjernman, Andreas Tjärnberg, Simon Wu, Karin Åkesson, Alexander K Shalek, Margaretha Stenmarker, Huan Zhang, Mika Gustafsson, Mikael Benson
Software Mentions: 7
Published: over 5 years ago
10.1038/s41598-019-46761-0
Lower Attentional Skills predict increased exploratory foraging patternsCited by: 16
Author(s): Charlotte Van den Driessche, Françoise Chevrier, Axel Cleeremans, Jérôme Sackur
Software Mentions: 7
Published: over 5 years ago
10.3390/ijms21010079
Current Projection Methods-Induced Biases at Subgroup Detection for Machine-Learning Based Data-Analysis of Biomedical DataCited by: 10
Author(s): Jörn Lötsch, Alfred Ultsch
Software Mentions: 6
Published: about 5 years ago
10.1186/s12920-021-01036-4
Multi-factor regulatory network and different clusters in hypertrophic obstructive cardiomyopathyCited by: 3
Author(s): Xianyu Qin, Lei Huang, Sicheng Chen, Shaoxian Chen, Pengju Wen, Yueheng Wu, Jian Zhuang
Software Mentions: 6
Published: over 3 years ago
10.7717/peerj.9478
Cellular heterogeneity map of diverse immune and stromal phenotypes within breast tumor microenvironmentCited by: 5
Author(s): Yuan Li, Zuhua Chen, Long Wu, Junjie Ye, Wenjing Tao
Software Mentions: 6
Published: over 4 years ago
10.1186/s13148-018-0463-6
Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsiaCited by: 60
Author(s): Katherine Leavey, Samantha L. Wilson, Shannon Bainbridge, Wendy P. Robinson, Brian Cox
Software Mentions: 6
Published: almost 7 years ago
10.1371/journal.pbio.3000799
5-Formylcytosine landscapes of human preimplantation embryos at single-cell resolutionCited by: 5
Author(s): Yun Gao, Lin Li, Peng Yuan, Fan Zhai, Yixuan Ren, Liying Yan, Rong Li, Ying Lian, Xiaohui Zhu, Xinglong Wu, Kehkooi Kee, Lu Wen, Jie Qiao, Fuchou Tang
Software Mentions: 5
Published: over 4 years ago
10.1002/jev2.12047
Single‐vesicle imaging and co‐localization analysis for tetraspanin profiling of individual extracellular vesiclesCited by: 38
Author(s): Chul‐Hi Han, Hyejin Kang, Johan Yi, Minsu Kang, Hyunjin Lee, Yongmin Kwon, Jae-Hun Jung, Jingeol Lee, Jaesung Park
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pcbi.1005335
Representing high throughput expression profiles via perturbation barcodes reveals compound targetsCited by: 22
Author(s): Tracey Filzen, Peter S. Kutchukian, Jeffrey D. Hermes, Jing Li, Matthew Tudor
Software Mentions: 3
Published: almost 8 years ago
10.1186/s13059-019-1892-z
Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell typeCited by: 39
Author(s): Irene Franco, Hafdís T. Helgadottir, Aldo Moggio, Malin Larsson, Peter Vrtačnik, Ada Johansson, Nina Norgren, Per Lundin, David Mas-Ponte, Jan Nordström, Torbjörn Lundgren, Peter Stenvinkel, Lars Wennberg, Fran Supek, Maria Eriksson
Software Mentions: 3
Published: about 5 years ago
10.3389/fmolb.2021.710623
Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin HexamersCited by: 3
Author(s): Khair Bux, Xiayu Shen, Muhammad Tariq, Junqi Yin, Syed Tarique Moin, Debsindhu Bhowmik, Shozeb Haider
Software Mentions: 3
Published: over 3 years ago
10.1186/s40478-019-0689-3
Genomic analysis demonstrates that histologically-defined astroblastomas are molecularly heterogeneous and that tumors with MN1 rearrangement exhibit the most favorable prognosisCited by: 50
Author(s): Norman L. Lehman, Aisulu Usubalieva, Tong Lin, Sariah J. Allen, Quynh Tran, Bret Mobley, Roger E. McLendon, Matthew Schniederjan, Maria Magdalena Georgescu, Marta Couce, Mohanpal S. Dulai, Jack M. Raisanen, Mousa Al Abbadi, Cheryl A. Palmer, Eyas M. Hattab, Brent A. Orr
Software Mentions: 3
Published: almost 6 years ago
10.1186/s12864-018-4512-5
High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysisCited by: 17
Author(s): Wanxin Wang, Lolita Penland, Özgün Gökçe, Derek Croote, Stephen R. Quake
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41396-020-0665-8
Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leavesCited by: 47
Author(s): Julián Regalado, Derek S. Lundberg, Oliver Deusch, Sonja Kersten, Talia L. Karasov, Karin Poersch, Gautam Shirsekar, Detlef Weigel
Software Mentions: 2
Published: over 4 years ago
10.3389/fbioe.2015.00035
Learning to Classify Organic and Conventional Wheat – A Machine Learning Driven Approach Using the MeltDB 2.0 Metabolomics Analysis PlatformCited by: 21
Author(s): Nikolas Kessler, Anja Bonte, Stefan P. Albaum, Paul Mäder, Monika Messmer, Alexander Goesmann, Karsten Niehaus, Georg Langenkämper, Tim Wilhelm Nattkemper
Software Mentions: 2
Published: almost 10 years ago
10.1038/s41598-020-57903-0
Adaptive Landscape Shaped by Core Endogenous Network Coordinates Complex Early Progenitor Fate Commitments in Embryonic PancreasCited by: 7
Author(s): Junqiang Wang, Ruoshi Yuan, Xiaomei Zhu, Ping Ao
Software Mentions: 2
Published: almost 5 years ago