bioconductor: SC3 | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1006361

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: over 6 years ago

10.12688/f1000research.15666.3

A systematic performance evaluation of clustering methods for single-cell RNA-seq data
Cited by: 33
Author(s): Angelo Duò, Mark D. Robinson, Charlotte Soneson
Software Mentions: 17
Published: about 4 years ago

10.1016/j.stem.2019.07.008

Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells
Cited by: 85
Author(s): Seungmin Han, J. Lynn Fink, David J. Jörg, Eunmin Lee, Min Kyu Yum, Lemonia Chatzeli, Sebastian R. Merker, Manon Josserand, Teodora Trendafilova, Amanda Andersson-Rolf, Catherine Dabrowska, Hyunki Kim, Ronald Naumann, Ji–Hyun Lee, Nobuo Sasaki, Richard L. Mort, Onur Basak, Hans Clevers, Daniel E. Stange, Anna Philpott, Jong Kim, Benjamin D. Simons, Bon‐Kyoung Koo
Software Mentions: 17
Published: about 5 years ago

10.1371/journal.pcbi.1006245

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Cited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago

10.3390/ijms22062822

A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research
Cited by: 6
Author(s): Efstathios Iason Vlachavas, Jonas Bohn, Frank Ückert, Sylvia Nürnberg
Software Mentions: 16
Published: over 3 years ago

10.1186/s12859-017-1994-0

PIVOT: platform for interactive analysis and visualization of transcriptomics data
Cited by: 30
Author(s): Qin Zhu, Stephen Fisher, Hannah Dueck, Sarah A. Middleton, Mugdha Khaladkar, Junhyong Kim
Software Mentions: 15
Published: almost 7 years ago

10.1186/s40478-020-0880-6

Single-nucleus RNA-seq identifies Huntington disease astrocyte states
Cited by: 147
Author(s): Osama Al‐Dalahmah, Alexander A. Sosunov, Ayesha Shaik, Kenneth Ofori, Yang Liu, Jean Paul Vonsattel, István Adorján, Vilas Menon, James E. Goldman
Software Mentions: 14
Published: almost 5 years ago

10.1186/s13059-017-1305-0

Splatter: simulation of single-cell RNA sequencing data
Cited by: 575
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 13
Published: about 7 years ago

10.7717/peerj.10469

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
Cited by: 5
Author(s): Daniel Dimitrov, Quan Gu
Software Mentions: 12
Published: almost 4 years ago

10.7554/eLife.48994

Self-assembling manifolds in single-cell RNA sequencing data
Cited by: 48
Author(s): Alexander J. Tarashansky, Yuan Xue, Pengyang Li, Stephen R. Quake, Bo Wang
Software Mentions: 12
Published: about 5 years ago

10.7554/eLife.38579

FoxA1 and FoxA2 drive gastric differentiation and suppress squamous identity in NKX2-1-negative lung cancer
Cited by: 52
Author(s): Soledad A. Camolotto, S. R. Pattabiraman, Timothy Mosbruger, Alex Jones, Veronika K Belova, Grace Orstad, Mitchell Streiff, Lydia Salmond, Chris Stubben, Klaus H. Kaestner, Eric L. Snyder
Software Mentions: 12
Published: almost 6 years ago

10.1093/bioinformatics/btz704

Spectrum: fast density-aware spectral clustering for single and multi-omic data
Cited by: 43
Author(s): Christopher R. John, David S. Watson, Michael R. Barnes, Costantino Pitzalis, Myles Lewis
Software Mentions: 10
Published: about 5 years ago

10.1186/s13059-020-02034-y

APEC: an accesson-based method for single-cell chromatin accessibility analysis
Cited by: 11
Author(s): Bin Li, Young Li, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin, Kun Qu
Software Mentions: 10
Published: over 4 years ago

10.1093/bioinformatics/btaa201

Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
Cited by: 37
Author(s): Meenakshi Venkatasubramanian, Kashish Chetal, Daniel Schnell, Gowtham Atluri, Nathan Salomonis
Software Mentions: 10
Published: over 4 years ago

10.7554/eLife.33105

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites
Cited by: 152
Author(s): Adam J. Reid, Arthur M. Talman, Hayley M. Bennett, Ana Gomes, Mandy Sanders, Christopher J. R. Illingworth, Oliver Billker, Matthew Berriman, Mara Lawniczak
Software Mentions: 9
Published: over 6 years ago

10.3390/ijms22031399

DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
Cited by: 5
Author(s): Salim Ghannoum, Waldir Leoncio Netto, Damiano Fantini, Benjamin Ragan-Kelley, Amirabbas Parizadeh, Emma Jonasson, Anders Ståhlberg, Hesso Farhan, Alvaro Köhn‐Luque
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.pcbi.1009064

coupleCoC+: An information-theoretic co-clustering-based transfer learning framework for the integrative analysis of single-cell genomic data
Cited by: 7
Author(s): Pengcheng Zeng, Zhixiang Lin
Software Mentions: 9
Published: over 3 years ago

10.1016/j.celrep.2020.108661

Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets
Cited by: 47
Author(s): Michael Fitzpatrick, Nicholas M. Provine, Lucy C. Garner, Kate Powell, Ali Amini, Sophie Irwin, Helen Ferry, Tim Ambrose, Peter J. Friend, Georgios Vrakas, Srikanth Reddy, Elizabeth Soilleux, Paul Klenerman, Philip Allan
Software Mentions: 9
Published: almost 4 years ago

10.1093/jmcb/mjaa052

Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts
Cited by: 18
Author(s): Lihua Zhang, Shihua Zhang
Software Mentions: 9
Published: about 4 years ago

10.3389/fgene.2021.665843

RFCell: A Gene Selection Approach for scRNA-seq Clustering Based on Permutation and Random Forest
Cited by: 3
Author(s): Yuan Zhao, Zhao-Yu Fang, Cui-Xiang Lin, Chao Deng, Yunpei Xu, Hongdong Li
Software Mentions: 8
Published: over 3 years ago

10.1016/j.molcel.2019.01.009

Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing
Cited by: 195
Author(s): Alba Rodríguez-Meira, Gemma Buck, Sally-Ann Clark, Benjamin Povinelli, Verónica Alcolea, Eleni Louka, Simon J. McGowan, Angela Hamblin, Nikolaos Sousos, Nikolaos Barkas, Alice Giustacchini, Bethan Psaila, Sten Eirik W. Jacobsen, Supat Thongjuea, Adam J. Mead
Software Mentions: 8
Published: over 5 years ago

10.1186/s13059-017-1188-0

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data
Cited by: 391
Author(s): Peijie Lin, Michael Troup, Joshua W. K. Ho
Software Mentions: 8
Published: over 7 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

10.3389/fnins.2018.00031

Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics
Cited by: 12
Author(s): Hyobin Jeong, Vijay Tiwari
Software Mentions: 8
Published: almost 7 years ago

10.3389/fcimb.2021.604129

Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage
Cited by: 6
Author(s): Kathrin Witmer, Farah A. Dahalan, Tom Metcalf, Arthur M. Talman, Virginia M. Howick, Mara K. N. Lawniczak
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2020.580373

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Cited by: 13
Author(s): Rym Ben‐Othman, Bing Cai, Aaron C. Liu, Natallia Varankovich, Daniel He, Travis M. Blimkie, Ahwon Lee, Erin E. Gill, M. A. Novotny, Brian D. Aevermann, Sibyl Drissler, Casey P. Shannon, Sarah McCann, Kim Marty, Gordean Bjornson, Rachel D. Edgar, David Lin, Nicole Gladish, Julia L. Maclsaac, Nelly Amenyogbe, Queenie Chan, Alba Llibre, Collin Joyce, Elise Landais, Khoa Le, Samantha M. Reiss, Wayne C. Koff, Colin Havenar-Daughton, Manraj K.S. Heran, Bippan S. Sangha, David R. Walt, Mel Krajden, Shane Crotty, Devin Sok, Bryan Briney, Dennis R. Burton, Darragh Duffy, Leonard J. Foster, William W. Mohn, Michael S. Kobor, Scott J. Tebbutt, Ryan R. Brinkman, Richard H. Scheuermann, Robert E. W. Hancock, Tobias R. Kollmann, Manish Sadarangani
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pgen.1008506

Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging
Cited by: 21
Author(s): Katelyn A. Walzer, Hélène Fradin, Liane Y. Emerson, David L. Corcoran, Jen‐Tsan Chi
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13059-021-02367-2

scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
Cited by: 40
Author(s): Tianyi Sun, Dongyuan Song, Jingyi Jessica Li, Jingyi Jessica Li
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1007788

Single-cell RNA-sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium
Cited by: 16
Author(s): Nhung Vuong, David P. Cook, Laura A. Forrest, Lauren E. Carter, Pascale Robineau-Charette, Joshua M. Kofsky, Kendra M. Hodgkinson, Barbara C. Vanderhyden
Software Mentions: 6
Published: about 6 years ago

10.1186/s12859-018-2226-y

DrImpute: imputing dropout events in single cell RNA sequencing data
Cited by: 243
Author(s): Wuming Gong, Il-Youp Kwak, Pruthvi Pota, Naoko Koyano-Nakagawa, Daniel J. Garry
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2019.00823

Weighted Gene Co-Expression Analyses Point to Long Non-Coding RNA Hub Genes at Different Schistosoma mansoni Life-Cycle Stages
Cited by: 19
Author(s): Lucas F. Maciel, David A. Morales-Vicente, Gilbert O. Silveira, Raphael O. Ribeiro, Giovanna G. O. Olberg, David S. Pires, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 6
Published: about 5 years ago

10.1016/j.immuni.2020.07.003

Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans
Cited by: 130
Author(s): Urszula Cytlak, Anastasia Resteu, Sarah Pagan, Kile Green, Paul Milne, Sheetal Maisuria, David McDonald, Gillian Hulme, Andrew Filby, Benjamin Carpenter, Rachel Queen, Sophie Hambleton, Rosie Hague, Hana Lango Allen, James Thaventhiran, Gina M. Doody, Matthew Collin, Venetia Bigley
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-020-67016-3

Recursive Consensus Clustering for novel subtype discovery from transcriptome data
Cited by: 5
Author(s): Pranali Sonpatki, Nameeta Shah
Software Mentions: 6
Published: over 4 years ago

10.3389/fgene.2021.666771

scGPS: Determining Cell States and Global Fate Potential of Subpopulations
Cited by: 1
Author(s): Michael Thompson, Maika Matsumoto, Tianqi Ma, Anne Senabouth, Nathan J. Palpant, Joseph E. Powell, Quan Nguyen
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-020-02032-0

Sampling time-dependent artifacts in single-cell genomics studies
Cited by: 50
Author(s): Ramón Massoni-Badosa, Giovanni Iacono, Cátia Moutinho, Marta Kulis, Núria Palau, Domenica Marchese, Javier Rodríguez-Ubreva, Esteban Ballestar, Gustavo Rodríguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elı́as Campo, Antonio Julià, José I. Martín‐Subero, Holger Heyn
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-020-02027-x

Accounting for cell type hierarchy in evaluating single cell RNA-seq clustering
Cited by: 19
Author(s): Zhijin Wu, Hao Wu
Software Mentions: 5
Published: over 4 years ago

10.1016/j.molmet.2017.02.007

Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing
Cited by: 125
Author(s): Brian Y.H. Lam, Irène Cimino, Joseph Polex-Wolf, Sara Kohnke, Debra Rimmington, Valentine P. Iyemere, Nicholas Heeley, Chiara Cossetti, Reiner Schulte, Luís R. Saraiva, Darren W. Logan, Clémence Blouet, Stephen O’Rahilly, Anthony P. Coll, Giles S.H. Yeo
Software Mentions: 5
Published: over 7 years ago

10.1038/s41419-021-03936-w

Valproic acid stimulates myogenesis in pluripotent stem cell-derived mesodermal progenitors in a NOTCH-dependent manner
Cited by: 9
Author(s): Natacha Breuls, Nefele Giarratana, Laura Yedigaryan, Gabriel Miró Garrido, Paolo Carai, Stéphane Heymans, Adrian Ranga, Christophe M. Deroose, Maurilio Sampaolesi
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2019.00371

High-Order Correlation Integration for Single-Cell or Bulk RNA-seq Data Analysis
Cited by: 9
Author(s): Hui Tang, Tao Zeng, Luonan Chen
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.30657

Wilms Tumor 1b defines a wound-specific sheath cell subpopulation associated with notochord repair
Cited by: 21
Author(s): Juan Carlos Lopez-Baez, Daniel J. Simpson, Laura Lleras Forero, Zhiqiang Zeng, Hannah Brunsdon, Angela Salzano, Alessandro Brombin, Cameron Wyatt, Witold M. Rybski, Leonie F. A. Huitema, Rodney M. Dale, Koichi Kawakami, Christoph Englert, Tamir Chandra, Stefan Schulte‐Merker, Nicholas D. Hastie, E. Elizabeth Patton
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.gpb.2018.10.003

SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data
Cited by: 29
Author(s): Xianwen Ren, Liangtao Zheng, Zemin Zhang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-66848-3

Identification of cell types from single cell data using stable clustering
Cited by: 24
Author(s): Azam Peyvandipour, Adib Shafi, Nafiseh Saberian, Sorin Drăghici
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-019-2952-9

Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data
Cited by: 19
Author(s): Savvas Kinalis, Finn Cilius Nielsen, Ole Winther, Frederik Otzen Bagger
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-020-03883-x

NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data
Cited by: 0
Author(s): Ruiyu Xiao, Guoshan Lu, Wanqian Guo, Shuilin Jin
Software Mentions: 4
Published: almost 4 years ago

10.1093/bioinformatics/btaa919

ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data
Cited by: 3
Author(s): Johannes Smolander, Sini Junttila, Mikko S Venäläinen, Laura L. Elo
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pcbi.1007040

PanoView: An iterative clustering method for single-cell RNA sequencing data
Cited by: 15
Author(s): Ming Hu, Dong Won Kim, Sheng Liu, Donald J. Zack, Seth Blackshaw, Jiang Qian
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1007488

Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process
Cited by: 9
Author(s): Jifan Shi, Tiejun Li, Luonan Chen, Kazuyuki Aihara
Software Mentions: 4
Published: about 5 years ago

10.3390/cells9091938

Detecting Interactive Gene Groups for Single-Cell RNA-Seq Data Based on Co-Expression Network Analysis and Subgraph Learning
Cited by: 10
Author(s): Xiucai Ye, Weihang Zhang, Yasunori Futamura, Tetsuya Sakurai
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-021-02281-7

scSorter: assigning cells to known cell types according to marker genes
Cited by: 43
Author(s): Hongqian Guo, Jun Li
Software Mentions: 4
Published: over 3 years ago

10.1038/s12276-020-0420-2

Single-cell multiomics: technologies and data analysis methods
Cited by: 239
Author(s): Jeongwoo Lee, Do Young Hyeon, Daehee Hwang
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2020.572242

EC-PGMGR: Ensemble Clustering Based on Probability Graphical Model With Graph Regularization for Single-Cell RNA-seq Data
Cited by: 4
Author(s): Youwen Zhu, Dexin Zhang, Xiaofei Zhang, Ming Yi, Le Ou-Yang, Mengyun Wu
Software Mentions: 4
Published: about 4 years ago

10.3390/genes11040377

Network-Based Single-Cell RNA-Seq Data Imputation Enhances Cell Type Identification
Cited by: 15
Author(s): Maryam Zand, Jianhua Ruan
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-021-02445-5

MultiK: an automated tool to determine optimal cluster numbers in single-cell RNA sequencing data
Cited by: 14
Author(s): Siyao Liu, Aatish Thennavan, Joseph P. Garay, J. S. Marron, Charles M. Perou
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-021-04033-7

Boosting scRNA-seq data clustering by cluster-aware feature weighting
Cited by: 2
Author(s): Ruiyi Li, Jihong Guan, Shuigeng Zhou
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-021-03957-4

Selecting single cell clustering parameter values using subsampling-based robustness metrics
Cited by: 35
Author(s): Ryan B. Patterson Cross, Ariel J. Levine, Vilas Menon
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12920-018-0433-z

Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method
Cited by: 31
Author(s): Yanglan Gan, Ning Li, Guobing Zou, Yongchang Xin, Jihong Guan
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41413-020-00109-x

Classification of four distinct osteoarthritis subtypes with a knee joint tissue transcriptome atlas
Cited by: 47
Author(s): Chunhui Yuan, Zongyou Pan, Kun Zhao, Jun Li, Zhaohan Sheng, Xudong Yao, Hua Liu, Xiaolei Zhang, Yang Yang, Dongsheng Yu, Yu Zhang, Yuzi Xu, Zhiyong Zhang, Tianlong Huang, Wanlu Liu, Hongwei Ouyang
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1006053

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa
Cited by: 29
Author(s): Huanan Zhang, Catherine A. A. Lee, Zhuliu Li, John Garbe, Cindy R. Eide, Raphael Petegrosso, Jakub Tolar
Software Mentions: 3
Published: over 6 years ago

10.1016/j.stem.2020.10.004

Three-Dimensional Human Alveolar Stem Cell Culture Models Reveal Infection Response to SARS-CoV-2
Cited by: 182
Author(s): Jeonghwan Youk, Taewoo Kim, Kelly V. Evans, Yoong Ki Jeong, Yong Suk Hur, Seon Pyo Hong, Je Hyoung Kim, Kijong Yi, Su Yeon Kim, Kwon Joong Na, Thomas Bleazard, Ho Min Kim, Mick D. Fellows, Krishnaa Mahbubani, Kourosh Saeb‐Parsy, Seon‐Young Kim, Young Tae Kim, Gou Young Koh, Boseung Choi, Young Seok Ju, Joo Hyeon Lee
Software Mentions: 3
Published: almost 4 years ago

10.1186/s41232-021-00170-x

Single-cell and spatial analyses of cancer cells: toward elucidating the molecular mechanisms of clonal evolution and drug resistance acquisition
Cited by: 18
Author(s): Satoi Nagasawa, Yukie Kashima, Ayako Suzuki, Yutaka Suzuki
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-22248-2

Single-cell RNA sequencing reveals developmental heterogeneity of blastomeres during major genome activation in bovine embryos
Cited by: 25
Author(s): Ilaria Lavagi, Stefan Krebs, Kilian Simmet, A. Beck, Valeri Zakhartchenko, Eckhard Wolf, Helmut Blum
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms21165797

Visualizing Single-Cell RNA-seq Data with Semisupervised Principal Component Analysis
Cited by: 10
Author(s): Zhenqiu Liu
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-72261-7

Single-cell RNA-seq identifies unique transcriptional landscapes of human nucleus pulposus and annulus fibrosus cells
Cited by: 34
Author(s): Lorenzo M. Fernandes, Nazir M. Khan, Camila M. Trochez, Meixue Duan, Martha Elena Díaz-Hernández, Steven M. Presciutti, Greg Gibson, Hicham Drissi
Software Mentions: 2
Published: about 4 years ago

10.3389/fgene.2020.604790

Sc-GPE: A Graph Partitioning-Based Cluster Ensemble Method for Single-Cell
Cited by: 8
Author(s): Xiaoshu Zhu, Jian Li, Hongdong Li, Miao Xie, Jianxin Wang
Software Mentions: 2
Published: almost 4 years ago

10.3389/fcell.2018.00028

Single Cell Multi-Omics Technology: Methodology and Application
Cited by: 114
Author(s): Youjin Hu, Qin An, Katherine M. Sheu, Brandon Trejo, Shuangshuang Fan, Ying Guo
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-020-0763-1

Recurrent pregnancy loss is associated with a pro-senescent decidual response during the peri-implantation window
Cited by: 132
Author(s): Emma S. Lucas, Pavle Vrljicak, Joanne Muter, Maria Diniz-da-Costa, Paul J. Brighton, Chow-Seng Kong, Julia Lipecki, Katherine Fishwick, Joshua Odendaal, Lauren J. Ewington, Siobhán Quenby, Sascha Ott, Jan J. Brosens
Software Mentions: 2
Published: almost 5 years ago

10.1093/gigascience/giz121

IKAP—Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis
Cited by: 14
Author(s): Yunching Chen, Abhilash Suresh, Chingiz Underbayev, Clare Sun, Komudi Singh, Fayaz Seifuddin, Adrian Wiestner, Mehdi Pirooznia
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0251461

Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states
Cited by: 2
Author(s): Kory R. Johnson, Barbara S. Mallon, Yang C. Fann, Kevin G. Chen
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-11-535

Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots
Cited by: 9
Author(s): Jérôme Gracy, Laurent Chiche
Software Mentions: 2
Published: about 14 years ago

10.1186/s12859-020-03797-8

Impact of data preprocessing on cell-type clustering based on single-cell RNA-seq data
Cited by: 9
Author(s): Chunxiang Wang, Xin Gao, Juntao Liu
Software Mentions: 2
Published: about 4 years ago

10.1016/j.celrep.2017.04.074

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment
Cited by: 73
Author(s): Kristina Kirschner, Tamir Chandra, Vladimir Yu Kiselev, David Flores-Santa Cruz, Iain C. Macaulay, Hyun Jun Park, Juan Li, David G. Kent, Rupa Kumar, Dean C. Pask, Tina L. Hamilton, Martin Hemberg, Wolf Reik, Anthony Green
Software Mentions: 1
Published: over 7 years ago

Projects: bioconductor: SC3

Papers Mentioning SC3 71