bioconductor: TSCAN | Projects | Ecosyste.ms: Papers

10.20517/jtgg.2020.51

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq
Cited 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

10.12688/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

10.3389/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: over 8 years ago

10.1186/s13059-020-02132-x

A systematic evaluation of single-cell RNA-sequencing imputation methods
Cited by: 156
Author(s): Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie Hicks
Software Mentions: 15
Published: over 4 years ago

10.3389/fgene.2019.00317

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis
Cited by: 549
Author(s): Geng Chen, Baitang Ning, Tieliu Shi
Software Mentions: 13
Published: over 5 years ago

10.1186/s13059-019-1898-6

Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
Cited by: 123
Author(s): Shuang Sun, Jiaqiang Zhu, Ying Ma, Xiang Zhou
Software Mentions: 13
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: about 6 years ago

10.1093/bioinformatics/btz889

<i>CellBench</i>: <i>R/Bioconductor</i> software for comparing single-cell RNA-seq analysis methods
Cited by: 17
Author(s): Shian Su, Luyi Tian, Xueyi Dong, Peter Hickey, Saskia Freytag, Matthew E. Ritchie
Software Mentions: 11
Published: about 5 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

10.3389/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: about 5 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

10.1371/journal.pcbi.1008205

Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data
Cited by: 43
Author(s): Tony Tran, Gary D. Bader
Software Mentions: 8
Published: over 4 years ago

10.1186/s12864-018-4649-2

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation
Cited by: 15
Author(s): Zhisong He, Qianhui Yu
Software Mentions: 8
Published: over 6 years ago

10.1186/s12864-018-4772-0

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
Cited by: 1,344
Author(s): Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit
Software Mentions: 8
Published: over 6 years ago

10.1038/s41598-020-80881-2

Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq
Cited by: 24
Author(s): Bin Wang, Yingyi Zhang, Tao Qing, Kaichen Xing, Jie Li, Timing Zhen, Sibo Zhu, Xi Zhan
Software Mentions: 8
Published: almost 4 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/fcvm.2018.00167

Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart
Cited by: 15
Author(s): Andrea Massaia, Patrícia Chaves, Sara Samari, Ricardo J. Miragaia, Kerstin B. Meyer, Sarah A. Teichmann, Michela Noseda
Software Mentions: 8
Published: about 6 years ago

10.3389/fcimb.2019.00392

Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution
Cited by: 13
Author(s): Regan J. Hayward, J. Wallis Marsh, Michael S. Humphrys, Wilhelmina M. Huston, Garry Myers
Software Mentions: 6
Published: about 5 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/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

10.1186/s40779-021-00336-1

Advances in single-cell sequencing: insights from organ transplantation
Cited by: 7
Author(s): Ying Wang, Jian‐Ye Wang, Angelika Schnieke, Konrad Fischer
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pbio.1002585

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process
Cited by: 192
Author(s): Richard Angélique, Boullu Loïs, Ulysse Herbach, Bonnafoux Arnaud, Valérie Morin, Elodie Vallin, Anissa Guillemin, Nan Gao, Gunawan Rudiyanto, Jérémie Cosette, Ophélie Arnaud, Jean-Jacques Kupiec, Thibault Espinasse, Sandrine Gonin-Giraud, Olivier Gandrillon
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13059-021-02341-y

PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data
Cited by: 22
Author(s): Dongyuan Song, Jingyi Jessica Li
Software Mentions: 5
Published: over 3 years ago

10.1186/s13073-017-0492-3

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
Cited by: 63
Author(s): Xun Zhu, Thomas Wolfgruber, Austin Tasato, Cédric Arisdakessian, David Garmire, Lana X. Garmire
Software Mentions: 5
Published: about 7 years ago

10.3390/ijms22179228

SARS-CoV-2 Impairs Dendritic Cells and Regulates DC-SIGN Gene Expression in Tissues
Cited by: 13
Author(s): Guoshuai Cai, Mulong Du, Yohan Bossé, Helmut Albrecht, Fei Qin, Xizhi Luo, X Michelle Androulakis, Chao Cheng, Mitzi Nagarkatti, Mitzi Nagarkatti, David C. Christiani, Michael L. Whitfield, Christopher I. Amos, Feifei Xiao
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2018.00108

Experimental Considerations for Single-Cell RNA Sequencing Approaches
Cited by: 125
Author(s): Quy Nguyen, Nicholas Pervolarakis, Kevin Nee, Kai Kessenbrock
Software Mentions: 4
Published: over 6 years ago

10.1002/iid3.362

What has single‐cell RNA sequencing revealed about microglial neuroimmunology?
Cited by: 15
Author(s): Norwin Kubick, Patrick C. Henckell Flournoy, Pavel Klimovich, Gina Manda, Michel‐Edwar Mickael
Software Mentions: 4
Published: about 4 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

10.3389/fmolb.2020.00209

Pinpointing Cell Identity in Time and Space
Cited by: 15
Author(s): Anca F. Savulescu, Caron Jacobs, Yutaka Negishi, L. Davignon, Musa M. Mhlanga
Software Mentions: 3
Published: over 4 years ago

10.1093/bioinformatics/bty664

GPseudoRank: a permutation sampler for single cell orderings
Cited by: 10
Author(s): Magdalena E Strauß, John E. Reid, Lorenz Wernisch
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.1005212

Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference
Cited by: 60
Author(s): Kieran R Campbell, Christopher Yau
Software Mentions: 3
Published: about 8 years ago

10.1093/bioinformatics/bty533

GrandPrix: scaling up the Bayesian GPLVM for single-cell data
Cited by: 37
Author(s): Sumon Ahmed, Magnus Rattray, Alexis Boukouvalas
Software Mentions: 3
Published: over 6 years ago

10.1038/s41392-020-00248-x

Nanoparticle enhanced combination therapy for stem-like progenitors defined by single-cell transcriptomics in chemotherapy-resistant osteosarcoma
Cited by: 24
Author(s): Li Wang, Xiaojia Huang, Xinru You, Tianqi Yi, Bing Lu, Jiali Liu, Guohao Lu, Minglin Ma, Changye Zou, Jun Wu, Wei Zhao
Software Mentions: 3
Published: about 4 years ago

10.1186/s12859-016-1109-3

SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation
Cited by: 49
Author(s): Hirotaka Matsumoto, Hisanori Kiryu
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-020-3448-3

Prediction model construction of mouse stem cell pluripotency using CpG and non-CpG DNA methylation markers
Cited by: 3
Author(s): Soobok Joe, Hojung Nam
Software Mentions: 3
Published: over 4 years ago

10.3390/e22111274

Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets
Cited by: 3
Author(s): Alexander Chervov, Jonathan Bac, Andreï Zinovyev
Software Mentions: 3
Published: about 4 years ago

10.1093/bioinformatics/bty498

A descriptive marker gene approach to single-cell pseudotime inference
Cited by: 35
Author(s): Kieran R Campbell, Christopher Yau
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.1007828

Predicting cell lineages using autoencoders and optimal transport
Cited by: 31
Author(s): Karren Yang, Karthik Damodaran, Saradha Venkatachalapathy, Ali C. Soylemezoglu, G. V. Shivashankar, Caroline Uhler
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2019.00500

Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells
Cited by: 25
Author(s): Emma Jonasson, Salim Ghannoum, Emma Persson, Jan Ch Karlsson, Thomas Kroneis, Erik Larsson, Göran Landberg, Anders Ståhlberg
Software Mentions: 2
Published: over 5 years ago

10.1093/bioinformatics/btx575

SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles
Cited by: 129
Author(s): Nan Gao, S. M. Minhaz Ud-Dean, Olivier Gandrillon, Rudiyanto Gunawan
Software Mentions: 2
Published: over 7 years ago

10.1186/s13195-019-0524-x

A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain
Cited by: 119
Author(s): Jorge L. Del‐Aguila, Zeran Li, Umber Dube, Kathie A. Mihindukulasuriya, John Budde, María Victoria Fernández, Laura Ibáñez, Joseph Bradley, Fengxian Wang, Kristy Bergmann, Richard Davenport, John C. Morris, David M. Holtzman, Richard J. Perrin, Bruno A. Benítez, Joseph D. Dougherty, Carlos Cruchaga, Oscar Harari
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22158109

Keratin Profiling by Single-Cell RNA-Sequencing Identifies Human Prostate Stem Cell Lineage Hierarchy and Cancer Stem-Like Cells
Cited by: 5
Author(s): Wen‐Yang Hu, Dongyan Hu, Lishi Xie, Larisa Nonn, Ranli Lu, Michael R. Abern, Toshihiro Shioda, Gail S. Prins
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-016-1175-6

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data
Cited by: 72
Author(s): David A. duVerle, Sohiya Yotsukura, Seitaro Nomura, Hiroyuki Aburatani, Koji Tsuda
Software Mentions: 2
Published: over 8 years ago

Projects: bioconductor: TSCAN

Papers Mentioning TSCAN 49