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: BASiCS

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

Bayesian Analysis of Single-Cell Sequencing data
1 version
Latest release: about 1 year ago
2 dependent packages
14,269 downloads total

Papers Mentioning BASiCS 21

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

10.20517/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

10.1002/1873-3468.12684

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/s13059-017-1305-0

Splatter: simulation of single-cell RNA sequencing data
Cited by: 575
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 13
Published: about 7 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/s13059-021-02329-8

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution
Cited by: 13
Author(s): Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti, Catalina A. Vallejos
Software Mentions: 11
Published: over 3 years ago

10.3389/fgene.2020.00041

Normalization Methods on Single-Cell RNA-seq Data: An Empirical Survey
Cited by: 46
Author(s): Nicholas Lytal, Ran Di, Lingling An
Software Mentions: 8
Published: almost 5 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

10.3389/fgene.2017.00062

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods
Cited by: 92
Author(s): Alessandra Dal Molin, Giacomo Baruzzo, Barbara Di Camillo
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pcbi.1009095

Identifying the combinatorial control of signal-dependent transcription factors
Cited by: 15
Author(s): Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-019-1874-1

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
Cited by: 2,100
Author(s): Christoph Hafemeister, Rahul Satija
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.cels.2018.06.011

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
Cited by: 63
Author(s): Nils Eling, Alison F. Richard, Sylvia Richardson, John C. Marioni, Catalina A. Vallejos
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-016-0930-3

Beyond comparisons of means: understanding changes in gene expression at the single-cell level
Cited by: 89
Author(s): Catalina A. Vallejos, Sylvia Richardson, John C. Marioni
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-020-07009-8

Bivalent genes that undergo transcriptional switching identify networks of key regulators of embryonic stem cell differentiation
Cited by: 6
Author(s): Ah-Jung Jeon, Greg Tucker‐Kellogg
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-020-03883-x

NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data
Cited by: 0
Author(s): Ruiyu Xiao, Guoshan Lu, Wanqian Guo, Shuilin Jin
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2021.650795

SMIXnorm: Fast and Accurate RNA-Seq Data Normalization for Formalin-Fixed Paraffin-Embedded Samples
Cited by: 0
Author(s): Yin Shen, Xiaowei Zhan, Bo Yao, Guanghua Xiao, Xinlei Wang, Yang Xie
Software Mentions: 3
Published: over 3 years ago

10.1016/j.cell.2021.02.002

Osteoclasts recycle via osteomorphs during RANKL-stimulated bone resorption
Cited by: 174
Author(s): Michelle M. McDonald, Weng Hua Khoo, Pei Ying Ng, Yue Xiao, Jad Zamerli, Peter Thatcher, Wunna Kyaw, Karrnan Pathmanandavel, Abigail K. Grootveld, Imogen Moran, Danyal Butt, Akira Nguyen, Alexander Corr, Sean Warren, Maté Biro, Natalie C. Butterfield, Siobhan E. Guilfoyle, Davide Komla-Ebri, Michael R.G. Dack, Hannah Dewhurst, John G. Logan, Yongxiao Li, Sindhu T. Mohanty, Niall M. Byrne, Rachael Terry, Marija K. Simic, Ryan C. Chai, Julian M.W. Quinn, Scott E. Youlten, Jessica A. Pettitt, David Abi‐Hanna, Rohit Jain, Wolfgang Weninger, Mischa Lundberg, Shuting Sun, Frank H. Ebetino, Paul Timpson, Woei Ming Lee, Paul A. Baldock, Michael J. Rogers, Robert Brink, Graham R. Williams, J. H. Duncan Bassett, John P. Kemp, Nathan J. Pavlos, Peter I. Croucher, Tri Giang Phan
Software Mentions: 3
Published: over 3 years ago

10.1007/s12551-019-00499-1

Bayesian statistical learning for big data biology
Cited by: 13
Author(s): Christopher Yau, Kieran R Campbell
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12974-021-02242-8

Interleukin-6 actions in the hypothalamus protects against obesity and is involved in the regulation of neurogenesis
Cited by: 18
Author(s): Vanessa Cristina Dias Bóbbo, Daiane F. Engel, Carlos Poblete Jara, Nelson F. Mendes, Roberta Haddad-Tóvolli, Thaís Paulino do Prado, Davi Sidarta-Oliveira, Joseane Morari, Lı́cio A. Velloso, Eliana P. Araújo
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pcbi.1004333

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
Cited by: 255
Author(s): Catalina A. Vallejos, John C. Marioni, Sylvia Richardson
Software Mentions: 2
Published: over 9 years ago

10.1016/j.cels.2019.08.003

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
Cited by: 7
Author(s): Nils Eling, Alison F. Richard, Sylvia Richardson, John C. Marioni, Catalina A. Vallejos
Software Mentions: 1
Published: about 5 years ago