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2020 – today
- 2023
[j9]Nicholas J. Eagles, Richard Wilton, Andrew E. Jaffe, Leonardo Collado-Torres
:
BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data. BMC Bioinform. 24(1): 340 (2023)- [j8]Sonia García-Ruíz, Emil K. Gustavsson, David Zhang, Regina H. Reynolds, Zhongbo Chen, Aine Fairbrother-Browne, Ana Luisa Gil-Martínez, Juan A. Botía, Leonardo Collado-Torres, Mina Ryten:
IntroVerse: a comprehensive database of introns across human tissues. Nucleic Acids Res. 51(D1): 167-178 (2023) - 2022
- [j7]Dario Righelli, Lukas M. Weber, Helena L. Crowell, Brenda Pardo, Leonardo Collado-Torres, Shila Ghazanfar, Aaron T. L. Lun, Stephanie C. Hicks, Davide Risso:
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinform. 38(11): 3128-3131 (2022) - 2021
- [j6]Christopher Wilks, Omar Ahmed, Daniel N. Baker, David Zhang, Leonardo Collado-Torres, Ben Langmead:
Megadepth: efficient coverage quantification for BigWigs and BAMs. Bioinform. 37(18): 3014-3016 (2021) - [j5]Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe, Leonardo Collado-Torres:
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. BMC Bioinform. 22(1): 224 (2021) - [j4]Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe, Leonardo Collado-Torres:
Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses. BMC Bioinform. 22(1): 381 (2021) - 2020
- [j3]Joselyn Chávez, Carmina Barberena-Jonas, Jesus E. Sotelo-Fonseca, José Alquicira-Hernández, Heladia Salgado, Leonardo Collado-Torres, Alejandro Reyes:
Programmatic access to bacterial regulatory networks with regutools. Bioinform. 36(16): 4532-4534 (2020)
2010 – 2019
- 2017
- [j2]Abhinav Nellore, Leonardo Collado-Torres, Andrew E. Jaffe, José Alquicira-Hernández, Christopher Wilks, Jacob Pritt, James Morton, Jeffrey T. Leek, Ben Langmead:
Rail-RNA: scalable analysis of RNA-seq splicing and coverage. Bioinform. 33(24): 4033-4040 (2017) - 2015
- [i1]Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek:
regionReport: Interactive reports for region-based analyses. F1000Research 4: 105 (2015) - 2011
- [j1]Socorro Gama-Castro, Heladia Salgado, Martín Peralta-Gil, Alberto Santos-Zavaleta, Luis Muñiz-Rascado, Hilda Solano-Lira, Verónica Jiménez-Jacinto, Verena Weiss, Jair S. García-Sotelo, Alejandra López-Fuentes, Liliana Porrón-Sotelo, Shirley Alquicira-Hernández, Alejandra Medina-Rivera, Irma Martínez-Flores, Kevin Alquicira-Hernández, Ruth Martínez-Adame, César Bonavides-Martínez, Juan Miranda-Ríos, Araceli M. Huerta, Alfredo Mendoza-Vargas, Leonardo Collado-Torres, Blanca Taboada, Leticia Vega-Alvarado, Maricela Olvera, Leticia Olvera, Ricardo Grande, Enrique Morett, Julio Collado-Vides:
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res. 39(Database-Issue): 98-105 (2011)
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