pypi: kmeans | Projects | Ecosyste.ms: Papers

10.7554/eLife.43966

Unified single-cell analysis of testis gene regulation and pathology in five mouse strains
Cited by: 91
Author(s): Min Jung, Daniel Wells, Jannette Rusch, Suhaira Ahmad, Jonathan Marchini, Simon Myers, Donald F. Conrad
Software Mentions: 22
Published: over 5 years ago

10.7717/peerj.5794

beadplexr: reproducible and automated analysis of multiplex bead assays
Cited by: 4
Author(s): Ulrik Stervbo, Timm H. Westhoff, Nina Babel
Software Mentions: 20
Published: about 6 years ago

10.1186/s12859-021-04054-2

CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data
Cited by: 13
Author(s): Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Wei‐Li Zhao, Xiao Jian Sun, Jinyan Huang
Software Mentions: 17
Published: over 3 years ago

10.1186/1471-2105-13-133

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling
Cited by: 30
Author(s): Julien Pelé, Jean Michel Bécu, Hervé Abdi, Marie Chabbert
Software Mentions: 14
Published: over 12 years ago

10.1186/s12859-021-04261-x

Machine learning-based prediction of survival prognosis in cervical cancer
Cited by: 16
Author(s): Dongyan Ding, Tingyuan Lang, Dongling Zou, Jianrong Tan, Jia Chen, Lei Zhou, Dong Wang, Rong Li, Yunzhe Li, Jingshu Liu, Cui Ma, Qi Zhou
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.ppat.1007945

Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype
Cited by: 28
Author(s): Bernd Hommel, Aude Sturny-Leclère, Stevenn Volant, Nathanaël Veluppillai, Magalie Duchateau, Chen-Hsin Albert Yu, Véronique Hourdel, Hugo Varet, Mariette Matondo, John R. Perfect, Arturo Casadevall, Françoise Dromer, Alexandre Alanio
Software Mentions: 10
Published: over 5 years ago

10.1186/1471-2105-11-503

Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering
Cited by: 54
Author(s): Eva Freyhult, Mattias Landfors, Jenny Önskog, Torgeir R. Hvidsten, Patrik Rydén
Software Mentions: 9
Published: about 14 years ago

10.3390/genes12020311

Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model
Cited by: 7
Author(s): Zhenqiu Liu
Software Mentions: 8
Published: over 3 years ago

10.1038/s41392-021-00729-7

Technological advances in cancer immunity: from immunogenomics to single-cell analysis and artificial intelligence
Cited by: 34
Author(s): Ying Xu, Guan-Hua Su, Ding Ma, Yi Xiao, Zhi-Ming Shao
Software Mentions: 8
Published: over 3 years ago

10.1038/s41380-020-0844-z

Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids
Cited by: 66
Author(s): Tomoyo Sawada, Thomas E. Chater, Yohei Sasagawa, Mika Yoshimura, Noriko Fujimori-Tonou, Kaori Tanaka, Kynon J.M. Benjamin, Apuã C.M. Paquola, Jennifer A. Erwin, Yukiko Goda, Itoshi Nikaido, Takeshi Kato
Software Mentions: 8
Published: over 4 years ago

10.1186/1471-2105-14-S16-S14

RMaNI: Regulatory Module Network Inference framework
Cited by: 6
Author(s): Piyush B. Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Mark A. Ragan
Software Mentions: 7
Published: about 11 years ago

10.3389/fninf.2018.00030

Information-Theoretical Analysis of EEG Microstate Sequences in Python
Cited by: 13
Author(s): Frederic von Wegner, Helmut Laufs
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0152454

Toward Objective, Morphology-Based Taxonomy: A Case Study on the Malagasy Nesomyrmex sikorai Species Group (Hymenoptera: Formicidae)
Cited by: 15
Author(s): Sándor Csősz, Brian L. Fisher
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0246656

Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile
Cited by: 10
Author(s): Daniel Kurth, Darío Elías, María Cecilia Rasuk, Manuel Contreras, Marı́a Eugenia Farı́as
Software Mentions: 6
Published: almost 4 years ago

10.3897/zookeys.603.8271

Taxonomic revision of the Malagasy Nesomyrmex madecassus species-group using a quantitative morphometric approach
Cited by: 4
Author(s): Sándor Csősz, Brian L. Fisher
Software Mentions: 6
Published: over 8 years ago

10.7717/peerj.1796

Taxonomic revision of the Malagasy members of theNesomyrmex angulatusspecies group using the automated morphological species delineation protocol NC-PART-clustering
Cited by: 14
Author(s): Sándor Csősz, Brian L. Fisher
Software Mentions: 6
Published: over 8 years ago

10.1186/1471-2105-11-279

Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver
Cited by: 12
Author(s): Tung Nguyen, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis
Software Mentions: 6
Published: over 14 years ago

10.1534/g3.120.401622

Alternative Splicing During the Chlamydomonas reinhardtii Cell Cycle
Cited by: 10
Author(s): Manishi Pandey, Gary D. Stormo, Susan K. Dutcher
Software Mentions: 5
Published: about 4 years ago

10.1093/bioinformatics/btaa613

Efficient weighted univariate clustering maps outstanding dysregulated genomic zones in human cancers
Cited by: 19
Author(s): Mingzhou Song, Hua Zhong
Software Mentions: 5
Published: over 4 years ago

10.1093/molbev/msw124

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution
Cited by: 107
Author(s): Michaela Kendall, Caroline Colijn
Software Mentions: 5
Published: over 8 years ago

10.7717/peerj.7362

DeepBindRG: a deep learning based method for estimating effective protein–ligand affinity
Cited by: 61
Author(s): Haiping Zhang, Linbu Liao, Konda Mani Saravanan, Peng Yin, Yanjie Wei
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0179613

A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells
Cited by: 7
Author(s): Benjamin Ulfenborg, Alexander Karlsson, Maria Riveiro, Caroline Améen, Karolina Åkesson, Christian X. Andersson, Peter Sartipy, Jane Synnergren
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-019-1917-7

A comparison framework and guideline of clustering methods for mass cytometry data
Cited by: 71
Author(s): Xiao Liu, Weichen Song, Brandon Wong, Ting Zhang, Shunying Yu, Guan Ning Lin, Yiyang Li
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pcbi.1008580

A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation
Cited by: 23
Author(s): Diego Vidaurre
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0166746

Deciphering Multiplicity of HIV-1C Infection: Transmission of Closely Related Multiple Viral Lineages
Cited by: 12
Author(s): Vlad Novitsky, Sikhulile Moyo, Rui Wang, Simani Gaseitsiwe, Myron Essex
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12920-020-00749-2

Analysis of H3K4me3 and H3K27me3 bivalent promotors in HER2+ breast cancer cell lines reveals variations depending on estrogen receptor status and significantly correlates with gene expression
Cited by: 6
Author(s): Damien Kaukonen, Riina Kaukonen, Lélia Polit, Bryan T. Hennessy, Riikka Lund, Stephen F. Madden
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2105-11-540

Circadian signatures in rat liver: from gene expression to pathways
Cited by: 24
Author(s): Meric Ovacik, Siddharth Sukumaran, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis
Software Mentions: 4
Published: about 14 years ago

10.1371/journal.pone.0172049

Discovery of temporal and disease association patterns in condition-specific hospital utilization rates
Cited by: 10
Author(s): Julian Haimovich, Arjun K. Venkatesh, Abbas Shojaee, Andreas Coppi, Frederick Warner, Shuxia Li, Harlan M. Krumholz
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-93162-3

Statistical and machine learning methods for analysis of multiplex protein data from a novel proximity extension assay in patients with ST-elevation myocardial infarction
Cited by: 1
Author(s): Emil Maag, Archana Kulasingam, Erik Lerkevang Grove, Kamilla Pedersen, Steen Dalby Kristensen, Anne‐Mette Hvas
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2014.00105

Assessing the functional consequence of loss of function variants using electronic medical record and large-scale genomics consortium efforts
Cited by: 3
Author(s): Patrick Sleiman, Jonathan P. Bradfield, Frank Mentch, Berta Almoguera, John J. Connolly, Hákon Hákonarson
Software Mentions: 3
Published: over 10 years ago

10.1186/s12859-019-2769-6

Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data
Cited by: 35
Author(s): Jiajie Peng, Xiaoyu Wang, Xuequn Shang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-021-04386-z

EvoLaps: a web interface to visualize continuous phylogeographic reconstructions
Cited by: 0
Author(s): François Chevenet, Denis Fargette, Stéphane Guindon, Anne‐Laure Bañuls
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1005875

Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
Cited by: 7
Author(s): Ye Henry Li, Dangna Li, Nikolay Samusik, Xiaowei Wang, Leying Guan, Garry P. Nolan, Wing Hung Wong
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.ppat.1009572

Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis
Cited by: 10
Author(s): Alonso Javier Pardal, Sophie J. M. Piquerez, Ana Dominguez-Ferreras, Lucas Frungillo, Emmanouil Mastorakis, Emma Reilly, David Latrasse, Lorenzo Concia, Selena Giménez-Ibáñez, Steven H. Spoel, Moussa Benhamed, Vardis Ntoukakis
Software Mentions: 3
Published: over 3 years ago

10.3389/fnhum.2020.561399

Mapping the Scene and Object Processing Networks by Intracranial EEG
Cited by: 6
Author(s): Kamil Vlček, Iveta Fajnerová, Tereza Nekovářová, Lukáš Hejtmánek, Radek Janča, Petr Ježdík, Adam Kalina, Martin Tomášek, Pavel Kršek, Jiří Hammer, Petr Marusič
Software Mentions: 2
Published: about 4 years ago

10.3390/genes8080201

Mutation Clusters from Cancer Exome
Cited by: 2
Author(s): Zura Kakushadze, Willie Yu
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-018-2442-5

Deblender: a semi−/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples
Cited by: 11
Author(s): Konstantina Dimitrakopoulou, Elisabeth Wik, Lars A. Akslen, Inge Jonassen
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0066104

Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics
Cited by: 27
Author(s): Becky M. Hess, Junfeng Xue, Lye Meng Markillie, Ron Taylor, H. Steven Wiley, Birgitte Kiær Ahring, Bryan Linggi
Software Mentions: 2
Published: over 11 years ago

10.4049/jimmunol.1402695

Regulatory T Cells in Melanoma Revisited by a Computational Clustering of FOXP3+ T Cell Subpopulations
Cited by: 19
Author(s): Hiroko Fujii, Julie Josse, Miki Tanioka, Yoshiki Miyachi, François Husson, M. Ono
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0007752

Glioblastoma Subclasses Can Be Defined by Activity among Signal Transduction Pathways and Associated Genomic Alterations
Cited by: 470
Author(s): Cameron Brennan, Hiroyuki Momota, Dolores Hambardzumyan, Tatsuya Ozawa, Adesh Tandon, Alicia Pedraza, Eric C. Holland
Software Mentions: 2
Published: about 15 years ago

10.7554/eLife.32373

Embryonic and postnatal neurogenesis produce functionally distinct subclasses of dopaminergic neuron
Cited by: 31
Author(s): Elisa Galliano, Eleonora Franzoni, Marine Breton, Annisa Chand, Darren J Byrne, Venkatesh N. Murthy, Matthew S. Grubb
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1006813

Predicting kinase inhibitors using bioactivity matrix derived informer sets
Cited by: 9
Author(s): Huikun Zhang, Spencer S. Ericksen, Ching-pei Lee, Gene E. Ananiev, Nathan Wlodarchak, Peng Yu, Julie C. Mitchell, Anthony Gitter, Stephen J. Wright, F. Michael Hoffmann, Scott A. Wildman, Michael A. Newton
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2021.689707

Constitutive TRIM22 Expression in the Respiratory Tract Confers a Pre-Existing Defence Against Influenza A Virus Infection
Cited by: 4
Author(s): Matthew Charman, Steven McFarlane, Joanna K. Wojtus, Elizabeth Sloan, Rebecca Dewar, Gail Leeming, Mohammed Al-Saadi, Laura Hunter, Miles W. Carroll, James Stewart, Paul Digard, Edward Hutchinson, Chris Boutell
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0255684

The water supply association analysis method in Shenzhen based on kmeans clustering discretization and apriori algorithm
Cited by: 7
Author(s): Xin Liu, Xuefeng Sang, Jiaxuan Chang, Yang Zheng, Yuping Han
Software Mentions: 2
Published: over 3 years ago

10.1186/s12885-015-1917-2

The combination of four molecular markers improves thyroid cancer cytologic diagnosis and patient management
Cited by: 36
Author(s): Federica Panebianco, Chiara Maria Mazzanti, Sara Tomei, Paolo Aretini, Sara Franceschi, Francesca Lessi, G Di Coscio, Generoso Bevilacqua, Ivo Marchetti
Software Mentions: 2
Published: about 9 years ago

10.3389/fncom.2013.00060

Kinematic decomposition and classification of octopus arm movements
Cited by: 26
Author(s): Ido Zelman, Myriam Titon, Yoram Yekutieli, Shlomi Hanassy, Binyamin Hochner, Tamar Flash
Software Mentions: 1
Published: almost 12 years ago

10.1098/rstb.2016.0021

Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii
Cited by: 27
Author(s): Rhys A. Farrer, Kerstin Voelz, Daniel A. Henk, Simon A. Johnston, Matthew C. Fisher, Robin C. May, Christina A. Cuomo
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1007729

Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion
Cited by: 37
Author(s): Emma Briggs, Kathryn Crouch, Leandro Lemgruber, Craig Lapsley, Richard McCulloch
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0058851

Identifying Gene Set Association Enrichment Using the Coefficient of Intrinsic Dependence
Cited by: 4
Author(s): Chen‐An Tsai, Liyu Liu
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0111251

Defining Mediterranean and Black Sea Biogeochemical Subprovinces and Synthetic Ocean Indicators Using Mesoscale Oceanographic Features
Cited by: 26
Author(s): Anne-Elise Nieblas, Kyla Drushka, Gabriel Reygondeau, Vincent Rossi, Hervé Demarcq, Laurent Dubroca, Sylvain Bonhommeau
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0141100

Transcriptomic Characterization of an Infection of Mycobacterium smegmatis by the Cluster A4 Mycobacteriophage Kampy
Cited by: 14
Author(s): Andrew D. Halleran, Samuel Clamons, Margaret S. Saha
Software Mentions: 1
Published: about 9 years ago

10.1186/1472-6963-13-333

Regional health care planning: a methodology to cluster facilities using community utilization patterns
Cited by: 22
Author(s): Paul L. Delamater, Ashton Shortridge, Joseph P. Messina
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-12-S2-S1

Sublineage structure analysis of Mycobacterium tuberculosis complex strains using multiple-biomarker tensors
Cited by: 14
Author(s): Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bülent Yener, Kristin P. Bennett
Software Mentions: 1
Published: almost 14 years ago

10.1002/epi4.12457

Evidence for long memory in focal seizure duration
Cited by: 3
Author(s): Joline M. Fan, Sharon Chiang, Vikram R. Rao
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.50374

Transcriptome dynamics of the Myxococcus xanthus multicellular developmental program
Cited by: 32
Author(s): José Muñoz‐Dorado, Aurelio Moraleda‐Muñoz, Francisco Javier Marcos‐Torres, Francisco Javier Contreras-Moreno, Ana Belén Martín‐Cuadrado, Jared M. Schrader, Penelope I. Higgs, Juana Pérez
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-015-0452-0

Data-intensive analysis of HIV mutations
Cited by: 1
Author(s): Mina Cintho Ozahata, Éster Cerdeira Sabino, Ricardo Sobhie Diaz, Roberto M. César, João Eduardo Ferreira
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep35185

An Optogenetic Demonstration of Motor Modularity in the Mammalian Spinal Cord
Cited by: 42
Author(s): Vittorio Caggiano, Vincent C. K. Cheung, Emilio Bizzi
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-020-74399-w

Multimodal deep learning models for early detection of Alzheimer’s disease stage
Cited by: 195
Author(s): Janani Venugopalan, Tong Li, Hamid Hassanzadeh, May D. Wang
Software Mentions: 1
Published: almost 4 years ago

10.3390/toxins11040189

Dinophysis Species and Diarrhetic Shellfish Toxins: 20 Years of Monitoring Program in Andalusia, South of Spain
Cited by: 18
Author(s): Raúl Gómez Fernández, Luz Mamán, David Jaén, Lourdes Fernández Fuentes, M Asunción Ocaña, M Mercedes Gordillo
Software Mentions: 1
Published: over 5 years ago

10.3897/zookeys.681.13187

Taxonomic revision of imitating carpenter ants, Camponotus subgenus Myrmopytia (Hymenoptera, Formicidae) of Madagascar, using morphometry and qualitative traits
Cited by: 7
Author(s): Nicole Rasoamanana, Sándor Csősz, Brian L. Fisher
Software Mentions: 1
Published: over 7 years ago

10.1186/1755-8794-2-10

Transcriptional profiling of mycobacterial antigen-induced responses in infants vaccinated with BCG at birth
Cited by: 29
Author(s): Helen A. Fletcher, Alana Keyser, Mark Bowmaker, Peter C. Sayles, Gilla Kaplan, G Hussey, Adrian V. S. Hill, Willem A. Hanekom
Software Mentions: 1
Published: over 15 years ago

Projects: pypi: kmeans

Papers Mentioning kmeans 62