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: M3Drop

https://packages.ecosyste.ms/registries/bioconductor.org/packages/M3Drop

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
1 version
Latest release: about 1 year ago
1 dependent package
34,195 downloads total

Papers Mentioning M3Drop 21

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: almost 4 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/s13059-019-1739-7

CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
Cited by: 33
Author(s): Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R. Salick, Joe Raymond, Ajamete Kaykas, Guglielmo Roma, Caroline Gubser Keller
Software Mentions: 13
Published: over 5 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

10.1016/j.cell.2021.04.048

Integrated analysis of multimodal single-cell data
Cited by: 4,423
Author(s): Yuhan Hao, Stephanie Hao, Erica Andersen‐Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Madeline Lee, Aaron J. Wilk, Charlotte A. Darby, Michael Zager, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, T.A. Stuart, Lamar M. Fleming, Bertrand Z. Yeung, Angela J. Rogers, Juliana McElrath, Catherine A. Blish, Raphaël Gottardo, Peter Smibert, Rahul Satija
Software Mentions: 13
Published: over 3 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: almost 5 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

10.1016/j.celrep.2020.108661

Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets
Cited by: 47
Author(s): Michael Fitzpatrick, Nicholas M. Provine, Lucy C. Garner, Kate Powell, Ali Amini, Sophie Irwin, Helen Ferry, Tim Ambrose, Peter J. Friend, Georgios Vrakas, Srikanth Reddy, Elizabeth Soilleux, Paul Klenerman, Philip Allan
Software Mentions: 9
Published: almost 4 years ago

10.15252/msb.20209620

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
Cited by: 166
Author(s): Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I. Jordan, Nir Yosef
Software Mentions: 9
Published: almost 4 years ago

10.7554/eLife.33105

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites
Cited by: 152
Author(s): Adam J. Reid, Arthur M. Talman, Hayley M. Bennett, Ana Gomes, Mandy Sanders, Christopher J. R. Illingworth, Oliver Billker, Matthew Berriman, Mara Lawniczak
Software Mentions: 9
Published: over 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

10.3389/fcimb.2021.604129

Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage
Cited by: 6
Author(s): Kathrin Witmer, Farah A. Dahalan, Tom Metcalf, Arthur M. Talman, Virginia M. Howick, Mara K. N. Lawniczak
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2018.01553

Single Cell RNA Sequencing of Rare Immune Cell Populations
Cited by: 88
Author(s): Akira Nguyen, Weng Hua Khoo, Imogen Moran, Peter I. Croucher, Tri Giang Phan
Software Mentions: 7
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: about 3 years ago

10.3390/ijms21186488

Lipid Stores and Lipid Metabolism Associated Gene Expression in Porcine and Bovine Parthenogenetic Embryos Revealed by Fluorescent Staining and RNA-seq
Cited by: 16
Author(s): Arkadiusz Kajdasz, Ewelina Warzych, Natalia Derebecka, Zofia E. Madeja, D. Lechniak, Joanna Wesoły, Piotr Pawlak
Software Mentions: 5
Published: about 4 years ago

10.1002/jbm4.10496

Single‐Cell <scp>RNA</scp>‐Sequencing Reveals the Breadth of Osteoblast Heterogeneity
Cited by: 11
Author(s): Hirotaka Yoshioka, Saki Okita, Masashi Nakano, Takeshi Minamizaki, Asako Nubukiyo, Yusuke Sotomaru, Edith Bonnelye, Katsuyuki Kozai, Kotaro Tanimoto, Jane E. Aubin, Yuji Yoshiko
Software Mentions: 4
Published: over 3 years ago

10.15252/msb.20188591

Widespread inter‐individual gene expression variability in <i>Arabidopsis thaliana</i>
Cited by: 48
Author(s): Sandra Cortijo, Zeynep Gökçe Gayretli Aydın, Sebastian E. Ahnert, James Locke
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-018-22248-2

Single-cell RNA sequencing reveals developmental heterogeneity of blastomeres during major genome activation in bovine embryos
Cited by: 25
Author(s): Ilaria Lavagi, Stefan Krebs, Kilian Simmet, A. Beck, Valeri Zakhartchenko, Eckhard Wolf, Helmut Blum
Software Mentions: 3
Published: over 6 years ago