Lori A. Shepherd

Orchestrating Spatial Transcriptomics Analysis with Bioconductor

The paper provides an open-source online book for analyzing spatial transcriptomics data using Bioconductor in R, with reproducible code and datasets.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.

Tximeta: reference sequence checksums for provenance identification in RNA-seq

Tximeta automatically identifies reference transcriptomes and gathers metadata for RNA-seq analysis using checksums, improving reproducibility and reducing errors.

BiocPkgTools: Toolkit for Mining the Bioconductor Package Ecosystem

BiocPkgTools provides a toolkit to access and analyze metadata from the Bioconductor package ecosystem, enabling downstream applications like data mining and graph analytics.

HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor

HMP16SData provides integrated 16S rRNA sequencing data from the Human Microbiome Project, enabling easier analysis for researchers with basic R skills.