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: TSCAN
https://packages.ecosyste.ms/registries/bioconductor.org/packages/TSCAN
Tools for Single-Cell Analysis
1 version
Latest release: about 1 year ago
3 dependent packages
34,387 downloads total
Papers Mentioning TSCAN 49
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
10.12688/f1000research.15666.3
A systematic performance evaluation of clustering methods for single-cell RNA-seq dataCited 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 ChallengesCited by: 101
Author(s): Olivier Poirion, Xun Zhu, Travers Ching, Lana X. Garmire
Software Mentions: 15
Published: about 8 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
10.3389/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
10.1186/s13059-019-1898-6
Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysisCited by: 123
Author(s): Shuang Sun, Jiaqiang Zhu, Ying Ma, Xiang Zhou
Software Mentions: 13
Published: almost 5 years ago
10.12688/f1000research.15809.2
Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing dataCited by: 90
Author(s): Saskia Freytag, Tian Li, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Software Mentions: 12
Published: almost 6 years ago
10.1093/bioinformatics/btz889
<i>CellBench</i>: <i>R/Bioconductor</i> software for comparing single-cell RNA-seq analysis methodsCited by: 17
Author(s): Shian Su, Luyi Tian, Xueyi Dong, Peter Hickey, Saskia Freytag, Matthew E. Ritchie
Software Mentions: 11
Published: almost 5 years ago
10.3390/ijms22031399
DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell TranscriptomicsCited 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 MethodsCited by: 56
Author(s): Monika Krzak, Yordan P. Raykov, Alexis Boukouvalas, Luisa Cutillo, Claudia Angelini
Software Mentions: 9
Published: almost 5 years ago
10.1186/s13046-021-01955-1
What are the applications of single-cell RNA sequencing in cancer research: a systematic reviewCited 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 dataCited by: 43
Author(s): Tony Tran, Gary D. Bader
Software Mentions: 8
Published: about 4 years ago
10.1186/s12864-018-4649-2
Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturationCited 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 transcriptomicsCited 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-seqCited 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 TranscriptomicsCited 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 HeartCited 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 ResolutionCited 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 dataCited 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 clusteringCited 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 transplantationCited 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 ProcessCited 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 dataCited 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 scientistsCited by: 63
Author(s): Xun Zhu, Thomas Wolfgruber, Austin Tasato, Cédric Arisdakessian, David Garmire, Lana X. Garmire
Software Mentions: 5
Published: almost 7 years ago
10.3390/ijms22179228
SARS-CoV-2 Impairs Dendritic Cells and Regulates DC-SIGN Gene Expression in TissuesCited 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: about 3 years ago
10.3389/fcell.2018.00108
Experimental Considerations for Single-Cell RNA Sequencing ApproachesCited by: 125
Author(s): Quy Nguyen, Nicholas Pervolarakis, Kevin Nee, Kai Kessenbrock
Software Mentions: 4
Published: about 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 processCited 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 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
10.1093/bioinformatics/bty664
GPseudoRank: a permutation sampler for single cell orderingsCited 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 InferenceCited 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 dataCited 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 osteosarcomaCited 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 differentiationCited 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 markersCited 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 DatasetsCited 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 inferenceCited 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 transportCited 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 CellsCited 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 profilesCited by: 129
Author(s): Nan Gao, S. M. Minhaz Ud-Dean, Olivier Gandrillon, Rudiyanto Gunawan
Software Mentions: 2
Published: about 7 years ago
10.1186/s13195-019-0524-x
A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brainCited 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 CellsCited 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 dataCited by: 72
Author(s): David A. duVerle, Sohiya Yotsukura, Seitaro Nomura, Hiroyuki Aburatani, Koji Tsuda
Software Mentions: 2
Published: about 8 years ago
10.3389/fcvm.2020.00042
Single Cell Analysis in Vascular BiologyCited by: 46
Author(s): Nicholas W. Chavkin, Karen K. Hirschi
Software Mentions: 2
Published: over 4 years ago
10.12688/wellcomeopenres.11087.1
Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzersCited by: 23
Author(s): Kieran R Campbell, Christopher Yau
Software Mentions: 2
Published: over 7 years ago
10.3389/fimmu.2021.711329
Unraveling the Heterogeneity and Ontogeny of Dendritic Cells Using Single-Cell RNA SequencingCited by: 13
Author(s): Binyao Chen, Lei Zhu, Shizhao Yang, Wenru Su
Software Mentions: 1
Published: about 3 years ago
10.15252/msb.20188552
Tree‐ensemble analysis assesses presence of multifurcations in single cell dataCited by: 2
Author(s): Will Macnair, Laura De Vargas Roditi, Stefan Ganscha, Manfred Claassen
Software Mentions: 1
Published: over 5 years ago
10.7554/eLife.20488
Discovering sparse transcription factor codes for cell states and state transitions during developmentCited by: 27
Author(s): Leon Furchtgott, Samuel Melton, Vilas Menon, Sharad Ramanathan
Software Mentions: 1
Published: over 7 years ago