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: tradeSeq

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

trajectory-based differential expression analysis for sequencing data
1 version
Latest release: about 1 year ago

Papers Mentioning tradeSeq 6

10.1186/s13148-021-01144-z

Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes
Cited by: 9
Author(s): Sara Di Persio, Elsa Leitão, Marius Wöste, Tobias Tekath, Jann‐Frederik Cremers, Martin Dugas, Xiaolin Liao, Gerd Meyer zu Hörste, Sabine Kliesch, Sandra Laurentino, Nina Neuhaus, Bernhard Horsthemke
Software Mentions: 8
Published: over 3 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 data
Cited by: 22
Author(s): Dongyuan Song, Jingyi Jessica Li
Software Mentions: 5
Published: over 3 years ago

10.1186/s13073-021-00933-8

Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19
Cited by: 71
Author(s): John F. Fullard, Hao-Chih Lee, Georgios Voloudakis, Shengbao Suo, Behnam Javidfar, Zhiping Shao, Cyril J. Peter, Wen Zhang, Shan Jiang, André Corvelo, Heather Wargnier, Emma Woodoff-Leith, Dushyant P. Purohit, Sadhna Ahuja, Nadejda M. Tsankova, Nathalie Jetté, Gabriel E. Hoffman, Schahram Akbarian, Mary Fowkes, John F. Crary, Guo‐Cheng Yuan, Panos Roussos
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-82914-w

Single-cell RNA sequencing reveals developmental heterogeneity among Plasmodium berghei sporozoites
Cited by: 17
Author(s): Anthony A Ruberto, Caitlin Bourke, Nicolas Mérienne, Thomas Obadia, Rogério Amino, Ivo Müeller
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pbio.3001394

Interplay between the EMT transcription factors ZEB1 and ZEB2 regulates hematopoietic stem and progenitor cell differentiation and hematopoietic lineage fidelity
Cited by: 12
Author(s): Jueqiong Wang, Carlos Farkas, Aïssa Benyoucef, Catherine Carmichael, Katharina Haigh, Nicholas C. Wong, Danny Huylebroeck, Marc P. Stemmler, Simone Brabletz, Thomas Brabletz, Christian M. Nefzger, Steven Goossens, Geert Berx, José M. Polo, Jody J. Haigh
Software Mentions: 1
Published: about 3 years ago

10.1126/sciadv.abg4755

XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment
Cited by: 60
Author(s): Youjin Lee, Derek Bogdanoff, Yutong Wang, George C. Hartoularos, Jonathan M. Woo, Cody T. Mowery, Hunter Nisonoff, David S. Lee, Yang Sun, James Lee, Sadaf Mehdizadeh, Joshua Cantlon, Eric Shifrut, David N. Ngyuen, Theodore L. Roth, Yun S. Song, Alexander Marson, Eric D. Chow, Chun Jimmie Ye
Software Mentions: 1
Published: over 3 years ago