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: bioconductor: scde

https://packages.ecosyste.ms/registries/bioconductor.org/packages/scde

Single Cell Differential Expression
1 version
Latest release: about 1 year ago
49,992 downloads total

Papers Mentioning scde 13

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: over 4 years ago

10.12688/f1000research.16198.2

scClustViz – Single-cell RNAseq cluster assessment and visualization
Cited by: 25
Author(s): Brendan T. Innes, Gary D. Bader
Software Mentions: 16
Published: over 5 years ago

10.1186/s13059-020-02116-x

Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Cited by: 107
Author(s): Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jingyu Fan, Xintao Qiu, Yingtian Xie, Clifford A. Meyer, Myles Brown, Ming Tang, Henry W. Long, Tao Liu, X. Shirley Liu
Software Mentions: 15
Published: over 4 years ago

10.1038/s41598-017-15525-z

Single-cell Co-expression Subnetwork Analysis
Cited by: 20
Author(s): Thomas E. Bartlett, Sören Müller, Aaron A. Diaz
Software Mentions: 9
Published: about 7 years ago

10.1242/dev.158501

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast
Cited by: 143
Author(s): Giuliano Giuseppe Stirparo, Thorsten Boroviak, Ge Guo, Jennifer Nichols, Austin Smith, Paul Bertone
Software Mentions: 9
Published: almost 7 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

10.1002/1878-0261.12569

Single‐cell RNA‐seq reveals the invasive trajectory and molecular cascades underlying glioblastoma progression
Cited by: 34
Author(s): Bo Pang, Jiu Hua Xu, Jing Hu, Fenghua Guo, Linyun Wan, Mingjiang Cheng, Lin Pang
Software Mentions: 7
Published: about 5 years ago

10.1242/dev.167833

Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development
Cited by: 145
Author(s): Thorsten Boroviak, Giuliano Giuseppe Stirparo, Sabine Dietmann, Irene Hernando-Herraez, Hisham Mohammed, Wolf Reik, Austin Smith, Erika Sasaki, Jennifer Nichols, Paul Bertone
Software Mentions: 6
Published: about 6 years ago

10.1093/gigascience/giy117

Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation
Cited by: 16
Author(s): Zhouchun Shang, Dongsheng Chen, Quanlei Wang, Shengpeng Wang, Qiuting Deng, Liang Wu, Chuanyu Liu, Xiangning Ding, Shiyou Wang, Junyan Zhong, Doudou Zhang, Xiaodong Cai, Shida Zhu, Huanming Yang, Longqi Liu, J. Lynn Fink, Fang Chen, Xiaoqing Liu, Zhengliang Gao, Xun Xu
Software Mentions: 5
Published: about 6 years ago

10.1016/j.devcel.2020.01.023

Functional Heterogeneity within the Developing Zebrafish Epicardium
Cited by: 46
Author(s): Michael Weinberger, Filipa C. Simões, Roger Patient, Tatjana Sauka‐Spengler, Paul R. Riley
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-019-5970-0

Single-cell RNA-seq of esophageal squamous cell carcinoma cell line with fractionated irradiation reveals radioresistant gene expression patterns
Cited by: 22
Author(s): Ling Yang, Xiaoyan Zhang, Qiang Hou, Ming Huang, Hongfang Zhang, Zhenzhen Jiang, Jing Yue, Shixiu Wu
Software Mentions: 4
Published: over 5 years ago

10.1093/molbev/msz290

Distinct Evolutionary Trajectories of Neuronal and Hair Cell Nicotinic Acetylcholine Receptors
Cited by: 26
Author(s): Irina Marcovich, Marcelo J. Moglie, Agustín Eduardo Carpaneto Freixas, Anabella Paola Trigila, Lucía F. Franchini, Paola V. Plazas, Marcela Lipovsek, Ana Belén Elgoyhen
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-017-1171-9

Single-cell transcriptome conservation in cryopreserved cells and tissues
Cited by: 131
Author(s): Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Elisabetta Mereu, María Méndez-Lago, Diego Adhemar Jaitin, Alberto Villanueva, August Vidal, Alex Martinez-Martí, Enriqueta Felip, Ana Vivancos, Hadas Keren‐Shaul, Simon Heath, Marta Gut, Ido Amit, Ivo Gut, Holger Heyn
Software Mentions: 2
Published: over 7 years ago