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: SAVER
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/SAVER
Single-Cell RNA-Seq Gene Expression Recovery
2 versions
Latest release: about 5 years ago
244 downloads last month
Papers Mentioning SAVER 40
10.15252/msb.20188746
Current best practices in single‐cell RNA‐seq analysis: a tutorialCited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Software Mentions: 20
Published: over 5 years ago
10.20517/jtgg.2020.51
Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seqCited by: 2
Author(s): Brandon Lieberman, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ning He, Yen‐Yi Ho, Josephine A. Taverna, Tim Hui-Ming Huang, Chun-Liang Chen
Software Mentions: 18
Published: almost 5 years ago
10.1186/s13059-020-02132-x
A systematic evaluation of single-cell RNA-sequencing imputation methodsCited by: 156
Author(s): Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie Hicks
Software Mentions: 15
Published: about 4 years ago
10.1186/s13059-017-1305-0
Splatter: simulation of single-cell RNA sequencing dataCited by: 575
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 13
Published: about 7 years ago
10.3389/fgene.2019.00317
Single-Cell RNA-Seq Technologies and Related Computational Data AnalysisCited by: 549
Author(s): Geng Chen, Baitang Ning, Tieliu Shi
Software Mentions: 13
Published: over 5 years ago
10.3389/fgene.2021.655536
Machine Intelligence in Single-Cell Data Analysis: Advances and New ChallengesCited by: 30
Author(s): Jiajia Li, Zusen Fan, Weiling Zhao, Xiaobo Zhou
Software Mentions: 12
Published: over 3 years ago
10.1186/s13059-021-02480-2
Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference constructionCited by: 16
Author(s): Wenjing Ma, Kenong Su, Hao Wu
Software Mentions: 12
Published: about 3 years ago
10.3390/genes11050532
Sparsity-Penalized Stacked Denoising Autoencoders for Imputing Single-Cell RNA-seq DataCited by: 9
Author(s): Weilai Chi, Minghua Deng
Software Mentions: 9
Published: over 4 years ago
10.1371/journal.pcbi.1009029
G2S3: A gene graph-based imputation method for single-cell RNA sequencing dataCited by: 7
Author(s): Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan, Zuoheng Wang
Software Mentions: 9
Published: over 3 years ago
10.1186/s13059-020-02096-y
Demystifying “drop-outs” in single-cell UMI dataCited by: 66
Author(s): Tae Hyun Kim, Xiang Zhou, Mengjie Chen
Software Mentions: 9
Published: over 4 years ago
10.1093/jmcb/mjaa052
Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropoutsCited by: 18
Author(s): Lihua Zhang, Shihua Zhang
Software Mentions: 9
Published: about 4 years ago
10.1186/s12864-019-5747-5
scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq dataCited by: 10
Author(s): Michael Fraser, Guoli Ji, Pengchao Ye, Yuqi Long, Xuesong Xiao, Shuchao Li, Yangfeng Su, Xiaohui Wu
Software Mentions: 8
Published: over 5 years ago
10.7554/eLife.65654
Quantitative control of noise in mammalian gene expression by dynamic histone regulationCited by: 2
Author(s): Tan D, Rui Chen, Yuejian Mo, Shu Gu, Jiao Ma, Wei Xu, Xibin Lu, Hongtao He, Fan Jiang, Weimin Fan, Yili Wang, Xi Chen, Wei Huang
Software Mentions: 8
Published: over 3 years ago
10.1186/s13059-019-1806-0
scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics dataCited by: 15
Author(s): Ruoxin Li, Gerald Quon
Software Mentions: 6
Published: about 5 years ago
10.1186/s13059-021-02400-4
mbImpute: an accurate and robust imputation method for microbiome dataCited by: 23
Author(s): Ruochen Jiang, Wei Vivian Li, Jingyi Jessica Li
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pcbi.1009118
SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq dataCited by: 6
Author(s): Jing Qi, Yang Zhou, Zhao Zhang, Shuilin Jin
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pcbi.1008569
Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics dataCited by: 16
Author(s): Andreas Tjärnberg, Omar Mahmood, Christopher Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel Christiaen, Richard Bonneau
Software Mentions: 6
Published: almost 4 years ago
10.1093/bioinformatics/btz726
bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing dataCited by: 59
Author(s): Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei
Software Mentions: 6
Published: about 5 years ago
10.1186/s13059-019-1837-6
DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq dataCited by: 162
Author(s): Cédric Arisdakessian, Olivier Poirion, Breck Yunits, Xun Zhu, Lana X. Garmire
Software Mentions: 6
Published: about 5 years ago
10.1186/s13045-020-01005-x
RNA sequencing: new technologies and applications in cancer researchCited by: 187
Author(s): Mingye Hong, Shuangping Tao, Ling Zhang, Li-Ting Diao, Xuanmei Huang, Shaohui Huang, Shu‐Juan Xie, Zhilong Xiao, Hua Zhang
Software Mentions: 5
Published: almost 4 years ago
10.1038/s41421-020-00236-z
Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy lossCited by: 74
Author(s): Chuang Guo, Pengfei Cai, Lina Jin, Qing Sha, Qiaoni Yu, Wen Zhang, Chen Jiang, Qian Liu, Dandan Zong, Kun Li, Jingwen Fang, Fangting Lu, Yanshi Wang, Daojing Li, Jun Lin, Lü Li, Zhutian Zeng, Xianhong Tong, Haiming Wei, Kun Qu
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.pcbi.1007794
Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysisCited by: 10
Author(s): Yuanchao Zhang, Man S. Kim, Erin R. Reichenberger, Benjamin Stear, Deanne Taylor
Software Mentions: 5
Published: over 4 years ago
10.1038/s12276-020-00499-2
Single-cell sequencing techniques from individual to multiomics analysesCited by: 116
Author(s): Yukie Kashima, Yoshitaka Sakamoto, Keiya Kaneko, Masahide Seki, Yutaka Suzuki, Ayako Suzuki
Software Mentions: 4
Published: about 4 years ago
10.1534/g3.120.401160
Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data AlignmentCited by: 31
Author(s): Yuheng Du, Qizhao Huang, Cédric Arisdakessian, Lana X. Garmire
Software Mentions: 4
Published: over 4 years ago
10.3390/genes11040377
Network-Based Single-Cell RNA-Seq Data Imputation Enhances Cell Type IdentificationCited by: 15
Author(s): Maryam Zand, Jianhua Ruan
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-018-1575-1
VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studiesCited by: 92
Author(s): Mengjie Chen, Xiang Zhou
Software Mentions: 4
Published: about 6 years ago
10.3389/fmolb.2020.00209
Pinpointing Cell Identity in Time and SpaceCited by: 15
Author(s): Anca F. Savulescu, Caron Jacobs, Yutaka Negishi, L. Davignon, Musa M. Mhlanga
Software Mentions: 3
Published: over 4 years ago
10.12688/f1000research.16613.2
False signals induced by single-cell imputationCited by: 99
Author(s): Tallulah Andrews, Martin Hemberg
Software Mentions: 3
Published: over 5 years ago
10.1186/s12859-020-03878-8
SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture modelCited by: 11
Author(s): Yan Zheng, Yuanke Zhong, Jialu Hu, Xuequn Shang
Software Mentions: 3
Published: almost 4 years ago
10.1186/s12859-020-03547-w
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq dataCited by: 2
Author(s): Qi Yang, Yang Guo, Huixin Jiao, Xuequn Shang
Software Mentions: 2
Published: over 4 years ago
10.1186/s12859-021-04022-w
PIKE-R2P: Protein–protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein predictionCited by: 7
Author(s): Xinnan Dai, Fan Xu, Shike Wang, Piyushkumar A. Mundra, Jie Zheng
Software Mentions: 2
Published: over 3 years ago
10.1016/j.csbj.2020.10.016
Probing infectious disease by single-cell RNA sequencing: Progresses and perspectivesCited by: 26
Author(s): Geyang Luo, Qian Gao, Shuye Zhang, Bo Yan
Software Mentions: 2
Published: almost 5 years ago
10.12688/f1000research.24163.2
Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistencyCited by: 0
Author(s): Maryam Zand, Jianhua Ruan
Software Mentions: 2
Published: almost 4 years ago
10.3389/fgene.2020.511286
Patterns, Profiles, and Parsimony: Dissecting Transcriptional Signatures From Minimal Single-Cell RNA-Seq Output With SALSACited by: 0
Author(s): Oswaldo A. Lozoya, Kathryn S. McClelland, Brian N. Papas, Jianliang Li, Hisayuki Yao
Software Mentions: 2
Published: about 4 years ago
10.1186/s13059-019-1681-8
SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq dataCited by: 83
Author(s): Tao Peng, Qin Zhu, Pengbin Yin, Kai Tan
Software Mentions: 2
Published: over 5 years ago
10.1186/s13063-021-05373-8
SAVER: sodium valproate for the epigenetic reprogramming of high-risk oral epithelial dysplasia—a phase II randomised control trial study protocolCited by: 4
Author(s): Caroline McCarthy, Joseph J. Sacco, Stefano Fedele, Michael Ho, Stephen Porter, Triantafillos Liloglou, Bill Greenhalf, Max Robinson, Bridget Young, Silvia Cicconi, Seema Chauhan, Binyam Tesfaye, Richard A. Jackson, Frances C Sherratt, Richard Shaw
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-019-56911-z
Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq dataCited by: 24
Author(s): Bettina Mieth, James R.F. Hockley, Nico Görnitz, Marina M.-C. Vidovic, Klaus Robert Müller, Alex Gutteridge, Daniel Ziemek
Software Mentions: 1
Published: almost 5 years ago
10.3389/fphys.2017.00277
Efficient Fetal-Maternal ECG Signal Separation from Two Channel Maternal Abdominal ECG via Diffusion-Based Channel SelectionCited by: 37
Author(s): Ruilin Li, Martin G. Frasch, Hau‐Tieng Wu
Software Mentions: 1
Published: over 7 years ago
10.3389/fonc.2021.676948
Current Insights and Advancements in Head and Neck Cancer: Emerging Biomarkers and Therapeutics with Cues from Single Cell and 3D Model Omics ProfilingCited by: 3
Author(s): Yashika Jawa, Pooja Yadav, Shruti Gupta, Sivapar V. Mathan, Jyoti Pandey, Ajay K. Saxena, Suneel Kateriya, Ashu Bhan Tiku, Neelima Mondal, Jaydeep Bhattacharya, Shandar Ahmad, Rupesh Chaturvedi, Rakesh K. Tyagi, Vibha Tandon, Rana P. Singh
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-020-07007-w
I-Impute: a self-consistent method to impute single cell RNA sequencing dataCited by: 4
Author(s): Xikang Feng, Lingxi Chen, Zishuai Wang, Shuai Cheng Li
Software Mentions: 1
Published: about 4 years ago