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: tximeta

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

Transcript Quantification Import with Automatic Metadata
1 version
Latest release: about 1 year ago
3 dependent packages
72,623 downloads total

Papers Mentioning tximeta 11

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: almost 5 years ago

10.1016/j.patter.2021.100322

The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: over 3 years ago

10.1371/journal.pcbi.1007664

Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Cited by: 122
Author(s): Michael I. Love, Charlotte Soneson, Peter Hickey, Lisa K. Johnson, Nicholas Pierce, Lori Shepherd, Martin Morgan, Rob Patro
Software Mentions: 19
Published: almost 5 years ago

10.1093/gigascience/giz149

Refgenie: a reference genome resource manager
Cited by: 28
Author(s): Michał Stolarczyk, Vincent Reuter, Jason P. Smith, Neal E. Magee, Nathan C. Sheffield
Software Mentions: 9
Published: almost 5 years ago

10.1534/g3.119.400185

ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data
Cited by: 35
Author(s): Stephany Orjuela, Ronald Huang, Katharina Hembach, Mark D. Robinson, Charlotte Soneson
Software Mentions: 8
Published: over 5 years ago

10.3389/fcell.2021.624053

“All-In-One” Genetic Tool Assessing Endometrial Receptivity for Personalized Screening of Female Sex Steroid Hormones
Cited by: 7
Author(s): Pavel Deryabin, А. П. Домнина, Inga V. Gorelova, M. V. Rulev, М. А. Petrosyan, Nikolay Nikolsky, Aleksandra Borodkina
Software Mentions: 7
Published: almost 4 years ago

10.1016/j.immuni.2020.03.011

Stromal Cells Covering Omental Fat-Associated Lymphoid Clusters Trigger Formation of Neutrophil Aggregates to Capture Peritoneal Contaminants
Cited by: 47
Author(s): Lucy H. Jackson-Jones, Peter Smith, Jordan Raymond Portman, Marlene S Magalhaes, Katie J. Mylonas, Matthieu Vermeren, Mark Nixon, Beth E. P. Henderson, Ross Dobie, Sonja Vermeren, Laura Denby, Neil C. Henderson, Damian J. Mole, C Benezech
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms21061938

Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis
Cited by: 8
Author(s): Dimitrios S. Kanakoglou, Theodora-Dafni Michalettou, Christina Vasileiou, Evangelos Gioukakis, Δωροθέα Μανέτα, Konstantinos Kyriakidis, Alexandros G. Georgakilas, Ioannis Michalopoulos
Software Mentions: 5
Published: almost 5 years ago

10.1007/s00395-021-00846-y

AMPKα1 deletion in myofibroblasts exacerbates post-myocardial infarction fibrosis by a connexin 43 mechanism
Cited by: 19
Author(s): Cécile Dufeys, Evangelos-Panagiotis Daskalopoulos, Diego Castanares-Zapatero, Simon J. Conway, Audrey Ginion, Caroline Bouzin, Jérôme Ambroise, Bertrand Bearzatto, Jean‐Luc Gala, Stéphane Heymans, Anna-Pia Papageorgiou, Stefan Vinckier, Julien Cumps, Jean‐Luc Balligand, Maarten Vanhaverbeke, Peter Sinnaeve, Stefan Janssens, Luc Bertrand, Christophe Beauloye, Sandrine Horman
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13104-021-05687-5

Genome-wide transcriptomic analysis of the forebrain of postnatal Slc13a4+/− mice
Cited by: 1
Author(s): Tracey J. Harvey, Raul Ayala Davila, Diana Vidovic, Sazia Sharmin, Michael Piper, David G. Simmons
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.666107

Monocytic Ontogeny of Regenerated Macrophages Characterizes the Mesotheliomagenic Responses to Carbon Nanotubes
Cited by: 4
Author(s): Micaela Orsi, Mihaly Palmai‐Pallag, Yousof Yakoub, Saloua Ibouraadaten, Michèle De Beukelaer, Caroline Bouzin, Bertrand Bearzatto, Jérôme Ambroise, Jean‐Luc Gala, Davide Brusa, Dominique Lison, François Huaux
Software Mentions: 1
Published: over 3 years ago