Bioconductor for Analysis and Comprehension of the Human Cell Atlas
Project Summary
This network’s collaborative effort enables the large community of users for the open source software R / Bioconductor to effectively access the Human Cell Atlas for statistical analysis, visualization, and novel scientific discovery.
Results & Resources
This group published 13 preprints describing 12 software packages that enable access to the Human Cell Atlas data, introduce new capabilities for emerging technologies, and implement novel high-throughput statistical and genomic analysis routines for scalable analytics and data visualization. These programs are available to the worldwide community of 850,000+ users with four additional packages under active development.
Papers:
- Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data
- mbkmeans: fast clustering for single-cell data using mini-batch k-means
- PsiNorm: a scalable normalization for single-cell RNA-seq data
- SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
- Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing
- A Systematic Evaluation of Single-cell RNA-sequencing Imputation Methods
- minicore: Fast scRNA-seq clustering with various distances
- Universal prediction of cell cycle position using transfer learning
- spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
- Long-read-tools.org: an interactive catalog of analysis methods for long-read sequencing data
- The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools
- Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
- A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
- Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles
Software: