bioconductor: SIMLR | Projects | Ecosyste.ms: Papers

10.12688/f1000research.11622.3

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
Cited by: 205
Author(s): Małgorzata Nowicka, Carsten Krieg, Helena L. Crowell, Lukas M. Weber, Felix J. Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P. Levesque, Mark D. Robinson
Software Mentions: 15
Published: over 5 years ago

10.3389/fgene.2016.00163

Single-Cell Transcriptomics Bioinformatics and Computational Challenges
Cited by: 101
Author(s): Olivier Poirion, Xun Zhu, Travers Ching, Lana X. Garmire
Software Mentions: 15
Published: about 8 years ago

10.1002/1873-3468.12684

Computational approaches for interpreting sc <scp>RNA</scp> ‐seq data
Cited by: 111
Author(s): Raghd Rostom, Valentine Svensson, Sarah A. Teichmann, Gozde Kar
Software Mentions: 14
Published: over 7 years ago

10.1186/s12859-021-04210-8

Contrastive self-supervised clustering of scRNA-seq data
Cited by: 28
Author(s): Madalina Ciortan, Matthieu Defrance
Software Mentions: 13
Published: over 3 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

10.12688/f1000research.15809.2

Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data
Cited by: 90
Author(s): Saskia Freytag, Tian Li, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Software Mentions: 12
Published: almost 6 years ago

10.1242/dev.177428

Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures
Cited by: 182
Author(s): Sandra Ruiz García, Marie Deprez, Kévin Lebrigand, Amélie Cavard, Agnès Paquet, Marie-Jeanne Arguel, Virginie Magnone, Marin Truchi, Ignacio Caballero, Sylvie Leroy, Charles‐Hugo Marquette, Brice Marcet, Pascal Barbry, Laure‐Emmanuelle Zaragosi
Software Mentions: 11
Published: about 5 years ago

10.3389/fgene.2019.00629

Single-Cell RNA Sequencing-Based Computational Analysis to Describe Disease Heterogeneity
Cited by: 23
Author(s): Tao Zeng, Hao Dai
Software Mentions: 10
Published: over 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/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

10.1371/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

10.3389/fgene.2019.01253

Benchmark and Parameter Sensitivity Analysis of Single-Cell RNA Sequencing Clustering Methods
Cited by: 56
Author(s): Monika Krzak, Yordan P. Raykov, Alexis Boukouvalas, Luisa Cutillo, Claudia Angelini
Software Mentions: 9
Published: almost 5 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

10.1186/s13046-021-01955-1

What are the applications of single-cell RNA sequencing in cancer research: a systematic review
Cited by: 28
Author(s): Lvyuan Li, Fang Xiong, Yumin Wang, Shanshan Zhang, Zhaojian Gong, Xiayu Li, Yi He, Lei Shi, Fuyan Wang, Qianjin Liao, Bo Xiang, Ming Zhou, Xiaoling Li, Yong Li, Guiyuan Li, Zhaoyang Zeng, Wei Xiong, Can Guo
Software Mentions: 9
Published: over 3 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

10.3390/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

10.1186/s12864-019-5747-5

scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data
Cited 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

10.3389/fgene.2020.00295

Single-Cell Transcriptome Data Clustering via Multinomial Modeling and Adaptive Fuzzy K-Means Algorithm
Cited by: 13
Author(s): Liang Chen, Weinan Wang, Yuyao Zhai, Minghua Deng
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0210571

Deterministic column subset selection for single-cell RNA-Seq
Cited by: 0
Author(s): Shannon R. McCurdy, Vasilis Ntranos, Lior Pachter
Software Mentions: 8
Published: almost 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

10.1186/s12885-021-08617-7

Precision treatment exploration of breast cancer based on heterogeneity analysis of lncRNAs at the single-cell level
Cited by: 3
Author(s): Yan Zhang, Denan Zhang, Qingkang Meng, Ziqi Liu, Hongbo Xie, Lei Liu, Fei Xu, Xiujie Chen
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2021.646936

A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data
Cited by: 44
Author(s): Ruizhi Xiang, Wencan Wang, Lei Yang, Shiyuan Wang, Chaohan Xu, Xiaowen Chen
Software Mentions: 5
Published: over 3 years ago

10.1093/gigascience/giz105

rCASC: reproducible classification analysis of single-cell sequencing data
Cited by: 24
Author(s): Luca Alessandrì, Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Martina Olivero, Greta Romano, Sergio Rabellino, Nicola Licheri, Gennaro De Libero, Luigia Pace, Raffaele Calogero
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.612670

Non-linear Normalization for Non-UMI Single Cell RNA-Seq
Cited by: 3
Author(s): Zhijin Wu, Kenong Su, Hao Wu
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-69552-4

Geographic variation in cardiometabolic risk factor prevalence explained by area-level disadvantage in the Illawarra-Shoalhaven region of the NSW, Australia
Cited by: 0
Author(s): Renin Toms, Darren J Mayne, Xiaoqi Feng, Andrew D Bonney
Software Mentions: 5
Published: over 4 years ago

10.26508/lsa.201900443

De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments
Cited by: 7
Author(s): Hyung Jun Woo, Boris Winterhoff, Timothy K. Starr, Constantin F. Aliferis, Jinhua Wang
Software Mentions: 4
Published: over 5 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

10.1093/bioinformatics/btz778

GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution
Cited by: 5
Author(s): Magdalena E Strauß, Paul Kirk, John E. Reid, Lorenz Wernisch
Software Mentions: 4
Published: about 5 years ago

10.1016/j.gpb.2018.08.003

VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder
Cited by: 159
Author(s): Dongfang Wang, Jin Gu
Software Mentions: 4
Published: about 6 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

10.3390/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

10.1371/journal.pone.0180583

Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data
Cited by: 24
Author(s): Chengchen Zhao, Shengen Hu, Xiao Huo, Yong Zhang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0223179

Geographic variation in cardiometabolic risk distribution: A cross-sectional study of 256,525 adult residents in the Illawarra-Shoalhaven region of the NSW, Australia
Cited by: 4
Author(s): Renin Toms, Darren J Mayne, Xiaoqi Feng, Andrew D Bonney
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2020.00407

An Adaptive Sparse Subspace Clustering for Cell Type Identification
Cited by: 15
Author(s): Ruiqing Zheng, Zhenlan Liang, Xiang Chen, Yu Tian, Chen Cao, Min Li
Software Mentions: 3
Published: over 4 years ago

10.3390/genes10020098

A Hybrid Clustering Algorithm for Identifying Cell Types from Single-Cell RNA-Seq Data
Cited by: 14
Author(s): Xiaoshu Zhu, Hongdong Li, Yunpei Xu, Lei Guo, Fang‐Xiang Wu, Guihua Duan, Jianxin Wang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-020-07038-3

Multi-scale supervised clustering-based feature selection for tumor classification and identification of biomarkers and targets on genomic data
Cited by: 17
Author(s): Da Xu, Jialin Zhang, Hanxiao Xu, Yusen Zhang, Wei Chen, Rui Gao, Matthias Dehmer
Software Mentions: 3
Published: about 4 years ago

10.1186/s12859-019-2817-2

A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification
Cited by: 7
Author(s): Douglas N. Abrams, Parveen Kumar, R. Krishna Murthy Karuturi, Joshy George
Software Mentions: 3
Published: over 5 years ago

10.1038/s41419-021-04092-x

Prognostic correlations with the microbiome of breast cancer subtypes
Cited by: 36
Author(s): Sagarika Banerjee, Zhi Wei, Tian Tian, Deepak Bose, Natalie Shih, Michael D. Feldman, Thaer Khoury, Angela De Michele, Erle S. Robertson
Software Mentions: 2
Published: about 3 years ago

10.3389/fninf.2018.00070

Unsupervised Manifold Learning Using High-Order Morphological Brain Networks Derived From T1-w MRI for Autism Diagnosis
Cited by: 63
Author(s): Mayssa Soussia, Islem Rekik
Software Mentions: 2
Published: about 6 years ago

10.1186/s12859-019-3179-5

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis
Cited by: 32
Author(s): Thomas A Geddes, Tai-Yun Kim, Lihao Nan, James G. Burchfield, Jean Yee Hwa Yang, Dacheng Tao, Pengyi Yang
Software Mentions: 2
Published: almost 5 years ago

Projects: bioconductor: SIMLR

Papers Mentioning SIMLR 40