bioconductor: SingleCellExperiment | Projects

10.1371/journal.pcbi.1006361

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: over 6 years ago

10.1186/s12864-020-06832-3

Seamless integration of image and molecular analysis for spatial transcriptomics workflows
Cited by: 121
Author(s): Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg
Software Mentions: 20
Published: over 4 years ago

10.1186/s12859-019-2879-1

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
Cited by: 146
Author(s): Fédérico Marini, Harald Binder
Software Mentions: 18
Published: over 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

10.1371/journal.pcbi.1006245

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Cited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago

10.12688/f1000research.22139.2

scRepertoire: An R-based toolkit for single-cell immune receptor analysis
Cited by: 121
Author(s): Nicholas Borcherding, Nicholas L. Bormann, Gloria Kraus
Software Mentions: 16
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

10.1371/journal.pcbi.1008625

mbkmeans: Fast clustering for single cell data using mini-batch k-means
Cited by: 27
Author(s): Stephanie C. Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom, Davide Risso
Software Mentions: 15
Published: almost 4 years ago

10.1093/gigascience/giy123

PiGx: reproducible genomics analysis pipelines with GNU Guix
Cited by: 51
Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Software Mentions: 15
Published: about 6 years ago

10.1186/s13059-020-02071-7

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Cited by: 56
Author(s): Ralph Patrick, David T. Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua W. K. Ho, Richard P. Harvey, Kitty Lo
Software Mentions: 13
Published: over 4 years ago

10.7554/eLife.62915

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data
Cited by: 9
Author(s): James W. Opzoomer, Jessica A Timms, Kevin Blighe, Thanos P. Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan G. Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca D. Ciccarelli, Peter J. Parker, Michaéla Fontenay, Paul R. Barber, James N. Arnold, Shahram Kordasti
Software Mentions: 13
Published: over 3 years ago

10.26508/lsa.202001004

CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data
Cited by: 21
Author(s): Almut Luetge, Joanna Zyprych-Walczak, Urszula Brykczynska Kunzmann, Helena L. Crowell, Daniela Calini, Dheeraj Malhotra, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: over 3 years ago

10.12688/f1000research.12122.1

Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference
Cited by: 14
Author(s): Fanny Perraudeau, Davide Risso, Kelly Street, Elizabeth Purdom, Sandrine Dudoit
Software Mentions: 12
Published: over 7 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

10.12688/f1000research.22969.2

clustifyr: an R package for automated single-cell RNA sequencing cluster classification
Cited by: 58
Author(s): Rui Fu, Austin E. Gillen, Ryan M. Sheridan, Chengzhe Tian, Michelle Daya, Yue Hao, Jay R. Hesselberth, Kent Riemondy
Software Mentions: 12
Published: over 4 years ago

10.1093/gigascience/giaa102

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
Cited by: 15
Author(s): Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, D. L. Clements, Fidel Ramírez, Graham Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan Manning, Léa Bellenger, Maria A. Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, Daniel Blankenberg, Rolf Backofen, Björn Grüning
Software Mentions: 12
Published: about 4 years ago

10.1371/journal.pcbi.1008585

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
Cited by: 43
Author(s): Charlotte Soneson, Avi Srivastava, Rob Patro, Michael Stadler
Software Mentions: 11
Published: almost 4 years ago

10.12688/f1000research.26669.2

TreeSummarizedExperiment: a S4 class for data with hierarchical structure
Cited by: 14
Author(s): Ronald Huang, Charlotte Soneson, Felix G.M. Ernst, Kévin Rue-Albrecht, Yu Guo, Stephanie C. Hicks, Mark D. Robinson
Software Mentions: 11
Published: over 3 years ago

10.1093/bioinformatics/btz889

CellBench: R/Bioconductor 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: almost 5 years ago

10.1074/mcp.TIR120.002155

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis
Cited by: 129
Author(s): Johannes Griss, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Kim Nguyen, Antonio Fabregat, Henning Hermjakob
Software Mentions: 11
Published: almost 4 years ago

10.1186/s12859-019-2797-2

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data
Cited by: 19
Author(s): Zhe Wang, Junming Hu, W. Evan Johnson, Joshua D. Campbell
Software Mentions: 10
Published: over 5 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

10.12688/f1000research.14966.1

iSEE: Interactive SummarizedExperiment Explorer
Cited by: 68
Author(s): Kévin Rue-Albrecht, Fédérico Marini, Charlotte Soneson, Aaron T. L. Lun
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pcbi.1006378

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Cited by: 45
Author(s): Davide Risso, Liam Purvis, Russell B. Fletcher, Diya Das, John Ngai, Sandrine Dudoit, Elizabeth Purdom
Software Mentions: 8
Published: about 6 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

10.1186/s13073-019-0615-0

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney
Cited by: 144
Author(s): Alexander N. Combes, Luke Zappia, Pei X. Er, Alicia Oshlack, Melissa H. Little
Software Mentions: 8
Published: almost 6 years ago

10.1016/j.cell.2021.01.002

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition
Cited by: 412
Author(s): Kevin Litchfield, James L. Reading, Clare Puttick, Krupa Thakkar, Chris Abbosh, Robert Bentham, Thomas B.K. Watkins, Rachel Rosenthal, Dhruva Biswas, Andrew Rowan, Emilia L. Lim, Maise Al Bakir, Virginia Turati, José Afonso Guerra-Assunção, Lucía Conde, Andrew J.S. Furness, Sunil Kumar Saini, Sine Reker Hadrup, Javier Herrero, Se‐Hoon Lee, Peter Van Loo, Tariq Enver, James Larkin, Matthew D. Hellmann, Samra Turajlic, Sergio A. Quezada, Nicholas McGranahan, Charles Swanton
Software Mentions: 7
Published: almost 4 years ago

10.1093/gigascience/giz087

ascend: R package for analysis of single-cell RNA-seq data
Cited by: 35
Author(s): Anne Senabouth, Samuel W. Lukowski, Jose Alquicira Hernandez, Stacey Andersen, Xin Mei, Quan Nguyen, Joseph E. Powell
Software Mentions: 7
Published: over 5 years ago

10.1084/jem.20200829

The mRNA m6A reader YTHDF2 suppresses proinflammatory pathways and sustains hematopoietic stem cell function
Cited by: 80
Author(s): Christopher Mapperley, Louie Van De Lagemaat, Hannah Lawson, Andrea Tavosanis, J Paris, Joana Campos, David Wotherspoon, Jozef Durko, Annika Sarapuu, Joong-Seon Choe, Ivayla Ivanova, Daniela Krause, Alex von Kriegsheim, Christian Much, Marcos Morgan, Richard I. Gregory, Adam J. Mead, Dónal O’Carroll, Kamil R. Kranc
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-021-07469-6

WASP: a versatile, web-accessible single cell RNA-Seq processing platform
Cited by: 5
Author(s): Andreas Hoek, Katharina Maibach, Ebru Özmen, Ana Ivonne Vazquez‐Armendariz, Jan Philipp Mengel, Torsten Hain, Susanne Herold, Alexander Goesmann
Software Mentions: 6
Published: over 3 years ago

10.1007/s13238-020-00720-y

Integrative analysis of in vivo recording with single-cell RNA-seq data reveals molecular properties of light-sensitive neurons in mouse V1
Cited by: 9
Author(s): Jianwei Liu, Mengdi Wang, Le Sun, Na Pan, Changjiang Zhang, Junjing Zhang, Zhentao Zuo, Sheng He, Qian Wu, Xiaoqun Wang
Software Mentions: 5
Published: over 4 years ago

10.1093/gigascience/giz047

Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood
Cited by: 24
Author(s): Yi Zhao, Xiao Li, Weihua Zhao, Jingwan Wang, Jun Yu, Ziyun Wan, Kai Gao, Gang Ye, Wang Xie, Bingbing Fan, Qinkai Wu, Bangwei Chen, Feng Xie, Jinghua Wu, Wei Zhang, Fang Chen, Huanming Yang, Jian Wang, Xun Xu, Bin Li, Shiping Liu, Yong Hou, Xiao Liu
Software Mentions: 4
Published: over 5 years ago

10.1111/cns.13396

Effect of intra‐ and inter‐tumoral heterogeneity on molecular characteristics of primary IDH‐wild type glioblastoma revealed by single‐cell analysis
Cited by: 22
Author(s): Zujian Xiong, Qi Yang, Xuejun Li
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2018.02523

Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice
Cited by: 4
Author(s): Wendi Bacon, Russell S. Hamilton, Ziyi Yu, Jens Kieckbusch, Dean Hawkes, Ada Maria Krzak, Chris Abell, Francesco Colucci, D. Stephen Charnock-Jones
Software Mentions: 4
Published: about 6 years ago

10.1093/bioinformatics/btaa1061

cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data
Cited by: 31
Author(s): Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers11111685

Intra-Patient Heterogeneity of Circulating Tumor Cells and Circulating Tumor DNA in Blood of Melanoma Patients
Cited by: 21
Author(s): Katharina Gorges, Lisa Wiltfang, Tobias M. Gorges, Alexander Sartori, Lina Hildebrandt, Laura Keller, Beate Volkmer, Sven Peine, Anna Babayan, Ingrid Moll, Stefan W. Schneider, Sören Twarock, Peter Mohr, Jens W. Fischer, Klaus Pantel
Software Mentions: 3
Published: about 5 years ago

Ecosyste.ms: Papers

Projects: bioconductor: SingleCellExperiment

Papers Mentioning SingleCellExperiment 36