regionReport: Interactive reports for region-level and feature-level genomic analyses

por Collado-Torres, Leonardo, Jaffe, Andrew E., Leek, Jeffrey T.
Publicado 2016

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor

por Collado-Torres, Leonardo, Nellore, Abhinav, Jaffe, Andrew E.
Publicado 2017

Improving the value of public RNA-seq expression data by phenotype prediction

por Ellis, Shannon E, Collado-Torres, Leonardo, Jaffe, Andrew, Leek, Jeffrey T
Publicado 2018

BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data

por Eagles, Nicholas J., Wilton, Richard, Jaffe, Andrew E., Collado-Torres, Leonardo
Publicado 2023

Megadepth: efficient coverage quantification for BigWigs and BAMs

por Wilks, Christopher, Ahmed, Omar, Baker, Daniel N, Zhang, David, Collado-Torres, Leonardo, Langmead, Ben
Publicado 2021

escheR: Unified multi-dimensional visualizations with Gestalt principles

por Guo, Boyi, Huuki-Myers, Louise A., Grant-Peters, Melissa, Collado-Torres, Leonardo, Hicks, Stephanie C.
Publicado 2023

SynGAP isoforms differentially regulate synaptic plasticity and dendritic development

por Araki, Yoichi, Hong, Ingie, Gamache, Timothy R, Ju, Shaowen, Collado-Torres, Leonardo, Shin, Joo Heon, Huganir, Richard L
Publicado 2020

Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments

por Sriworarat, Chaichontat, Nguyen, Annie, Eagles, Nicholas J., Collado-Torres, Leonardo, Martinowich, Keri, Maynard, Kristen R., Hicks, Stephanie C.
Publicado 2023

Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single cell RNA-sequencing datasets

por Maden, Sean K., Kwon, Sang Ho, Huuki-Myers, Louise A., Collado-Torres, Leonardo, Hicks, Stephanie C., Maynard, Kristen R.
Publicado 2023

Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue

por Huuki-Myers, Louise A., Montgomery, Kelsey D., Kwon, Sang Ho, Page, Stephanie C., Hicks, Stephanie C., Maynard, Kristen R., Collado-Torres, Leonardo
Publicado 2023

Flexible expressed region analysis for RNA-seq with derfinder

por Collado-Torres, Leonardo, Nellore, Abhinav, Frazee, Alyssa C., Wilks, Christopher, Love, Michael I., Langmead, Ben, Irizarry, Rafael A., Leek, Jeffrey T., Jaffe, Andrew E.
Publicado 2017

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

por Righelli, Dario, Weber, Lukas M, Crowell, Helena L, Pardo, Brenda, Collado-Torres, Leonardo, Ghazanfar, Shila, Lun, Aaron T L, Hicks, Stephanie C, Risso, Davide
Publicado 2022

Comparison of gene expression in living and postmortem human brain

por Collado-Torres, Leonardo, Klei, Lambertus, Liu, Chunyu, Kleinman, Joel E., Hyde, Thomas M., Geschwind, Daniel H., Gandal, Michael J., Devlin, Bernie, Weinberger, Daniel R.
Publicado 2023

Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses

por Kuri-Magaña, Helena, Collado-Torres, Leonardo, Jaffe, Andrew E., Valdovinos-Torres, Humberto, Ovilla-Muñoz, Marbella, Téllez-Sosa, Juan, Bonifaz, Laura C., Martínez-Barnetche, Jesús
Publicado 2018

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

por Pardo, Brenda, Spangler, Abby, Weber, Lukas M., Page, Stephanie C., Hicks, Stephanie C., Jaffe, Andrew E., Martinowich, Keri, Maynard, Kristen R., Collado-Torres, Leonardo
Publicado 2022

IntroVerse: a comprehensive database of introns across human tissues

por García-Ruiz, Sonia, Gustavsson, Emil K, Zhang, David, Reynolds, Regina H, Chen, Zhongbo, Fairbrother-Browne, Aine, Gil-Martínez, Ana Luisa, Botia, Juan A, Collado-Torres, Leonardo, Ryten, Mina
Publicado 2022

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

por Nellore, Abhinav, Jaffe, Andrew E., Fortin, Jean-Philippe, Alquicira-Hernández, José, Collado-Torres, Leonardo, Wang, Siruo, Phillips III, Robert A., Karbhari, Nishika, Hansen, Kasper D., Langmead, Ben, Leek, Jeffrey T.
Publicado 2016

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

por Wright, Carrie, Rajpurohit, Anandita, Burke, Emily E., Williams, Courtney, Collado-Torres, Leonardo, Kimos, Martha, Brandon, Nicholas J., Cross, Alan J., Jaffe, Andrew E., Weinberger, Daniel R., Shin, Joo Heon
Publicado 2019

Developmental regulation of human cortex transcription and its clinical relevance at base resolution

por Jaffe, Andrew E., Shin, Jooheon, Collado-Torres, Leonardo, Leek, Jeffrey T., Tao, Ran, Li, Chao, Gao, Yuan, Jia, Yankai, Maher, Brady J., Hyde, Thomas M., Kleinman, Joel E., Weinberger, Daniel R.
Publicado 2014

Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders

por Zhang, David, Guelfi, Sebastian, Garcia-Ruiz, Sonia, Costa, Beatrice, Reynolds, Regina H., D’Sa, Karishma, Liu, Wenfei, Courtin, Thomas, Peterson, Amy, Jaffe, Andrew E., Hardy, John, Botía, Juan A., Collado-Torres, Leonardo, Ryten, Mina
Publicado 2020