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: DeconRNASeq

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

Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
1 version
Latest release: about 1 year ago
32,983 downloads total

Papers Mentioning DeconRNASeq 23

10.1016/j.xpro.2020.100085

Protocol for Identification and Removal of Doublets with DoubletDecon
Cited by: 7
Author(s): Erica A. K. DePasquale, Daniel Schnell, Kashish Chetal, Nathan Salomonis
Software Mentions: 25
Published: about 4 years ago

10.3390/cancers11091248

Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological Features
Cited by: 28
Author(s): Sabino Russi, Giovanni Calice, Vitalba Ruggieri, Simona Laurino, Francesco La Rocca, Elena Amendola, Cinzia Lapadula, Debora Compare, Gerardo Nardone, Pellegrino Musto, Mario De Felice, Geppino Falco, Pietro Zoppoli
Software Mentions: 12
Published: about 5 years ago

10.1186/s12974-018-1113-9

Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness
Cited by: 45
Author(s): David G. Ashbrook, Benjamin Hing, Lindsay T. Michalovicz, Kimberly A. Kelly, Julie V. Miller, Wilfred C. de Vega, Diane B. Miller, Gordon Broderick, James P. O’Callaghan, Patrick O. McGowan
Software Mentions: 9
Published: over 6 years ago

10.1038/s41392-021-00729-7

Technological advances in cancer immunity: from immunogenomics to single-cell analysis and artificial intelligence
Cited by: 34
Author(s): Ying Xu, Guan-Hua Su, Ding Ma, Yi Xiao, Zhi-Ming Shao
Software Mentions: 8
Published: about 3 years ago

10.3390/cells8101161

An Efficient and Flexible Method for Deconvoluting Bulk RNA-Seq Data with Single-Cell RNA-Seq Data
Cited by: 15
Author(s): Xifang Sun, Shuang Sun, Sheng Yang
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0224693

ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells
Cited by: 15
Author(s): Samuel A. Danziger, David L. Gibbs, Ilya Shmulevich, Mark McConnell, Matthew Trotter, Frank Schmitz, David J Reiss, Alexander V. Ratushny
Software Mentions: 7
Published: almost 5 years ago

10.1016/j.stem.2019.07.009

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency
Cited by: 27
Author(s): Hannah Stuart, Giuliano Giuseppe Stirparo, Tim Lohoff, Lawrence E. Bates, Masaki Kinoshita, Chee Lim, Elsa Joana Sousa, Katsiaryna Maskalenka, Aliaksandra Radzisheuskaya, Andrew A. Malcolm, Mariana R. P. Alves, Rebecca L. Lloyd, Sonia Nestorowa, Peter Humphreys, William Mansfield, Wolf Reik, Paul Bertone, Jennifer Nichols, Berthold Göttgens, José C.R. Silva
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2020.00392

DeconPeaker, a Deconvolution Model to Identify Cell Types Based on Chromatin Accessibility in ATAC-Seq Data of Mixture Samples
Cited by: 20
Author(s): Huamei Li, Ingo G. H. Schmidt‐Wolf, Kun Luo, Zhaohui S. Qin, Xiao Sun, Hongde Liu
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-015-0597-x

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles
Cited by: 30
Author(s): Catalina Anghel, Gerald Quon, Syed Haider, Francis Nguyen, Amit G. Deshwar, Quaid Morris, Paul C. Boutros
Software Mentions: 5
Published: over 9 years ago

10.1016/j.celrep.2019.09.082

DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data
Cited by: 120
Author(s): Erica A. K. DePasquale, Daniel Schnell, Pieter-Jan Van Camp, Íñigo Valiente-Alandí, Burns C. Blaxall, H. Leighton Grimes, Harinder Singh, Nathan Salomonis
Software Mentions: 5
Published: about 5 years ago

10.1002/advs.201902880

ImmuCellAI: A Unique Method for Comprehensive T‐Cell Subsets Abundance Prediction and its Application in Cancer Immunotherapy
Cited by: 479
Author(s): Ya-Ru Miao, Qiong Zhang, Qian Lei, Mei Luo, Gui-Yan Xie, Hongxiang Wang, An‐Yuan Guo
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2018.01286

seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data
Cited by: 61
Author(s): Ziyi Chen, Lijun Quan, Anfei Huang, Qiang Zhao, Yuan Yao, Xuye Yuan, Qin Shen, Jingzhe Shang, Yinyin Ben, F. Xiao-Feng Qin, Aiping Wu
Software Mentions: 5
Published: over 6 years ago

10.1093/gigascience/giab002

The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data
Cited by: 26
Author(s): Brian B. Nadel, David Lopez, Dennis Montoya, Feiyang Ma, Hannah Waddel, Misha M Khan, Serghei Mangul, Matteo Pellegrini
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-021-02290-6

A benchmark for RNA-seq deconvolution analysis under dynamic testing environments
Cited by: 46
Author(s): Haijing Jin, Zhandong Liu
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-017-0458-5

Post-mortem molecular profiling of three psychiatric disorders
Cited by: 133
Author(s): Ryne C. Ramaker, Kevin M. Bowling, Brittany N. Lasseigne, Megan Hastings Hagenauer, Andrew A. Hardigan, Nicholas S. Davis, Jason Gertz, Preston Cartagena, David Walsh, Marquis P. Vawter, Edward G. Jones, Alan F. Schatzberg, Jack D. Barchas, Stanley J. Watson, Blynn G. Bunney, Huda Akil, William E. Bunney, Jun Z. Li, Sara J. Cooper, R Myers
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.26476

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data
Cited by: 674
Author(s): Julien Racle, Kaat de Jonge, Petra Baumgaertner, Daniel E. Speiser, David Gfeller
Software Mentions: 3
Published: almost 7 years ago

10.1007/s00262-018-2150-z

Quantifying tumor-infiltrating immune cells from transcriptomics data
Cited by: 258
Author(s): Francesca Finotello, Zlatko Trajanoski
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0193067

Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues
Cited by: 13
Author(s): Lee A. Newberg, Xiaowei Chen, Chinnappa D. Kodira, Maria I. Zavodszky
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-62330-2

Semi-CAM: A semi-supervised deconvolution method for bulk transcriptomic data with partial marker gene information
Cited by: 3
Author(s): Dong Li, Avinash Kollipara, Toni Darville, Fei Zou, Xiaojing Zheng
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-018-2442-5

Deblender: a semi−/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples
Cited by: 11
Author(s): Konstantina Dimitrakopoulou, Elisabeth Wik, Lars A. Akslen, Inge Jonassen
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40246-018-0161-7

Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness
Cited by: 9
Author(s): Kobi Perl, Ron Shamir, Karen B. Avraham
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-021-04187-4

A novel method for predicting cell abundance based on single-cell RNA-seq data
Cited by: 7
Author(s): Jiajie Peng, Lu Han, Xuequn Shang
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2018.00638

Immunization Elicits Antigen-Specific Antibody Sequestration in Dorsal Root Ganglia Sensory Neurons
Cited by: 14
Author(s): Manojkumar Gunasekaran, Prodyot K. Chatterjee, Andrew Shih, Gavin H. Imperato, Meghan Addorisio, Gopal Kumar, Annette Lee, John Graf, Dan E. Meyer, Michael Marino, Christopher M. Puleo, Jeffrey Ashe, Maureen A. Cox, Tak W. Mak, Chad Bouton, Barbara Sherry, Betty Diamond, Ulf Andersson, Thomas R. Coleman, Christine N. Metz, Kevin J. Tracey, Sangeeta S. Chavan
Software Mentions: 2
Published: over 6 years ago