Stars
Biological sequence analysis for the modern age.
Method for inferring path posterior probabilities and abundances from pangenome graph read alignments
Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
Code repository for the snRNA-seq cross-tissue atlas project
Repo for analysis of SMM DNA + RNA data.
Website for checking a variant's SpliceAI, Pangolin, and other scores:
Deep probabilistic analysis of single-cell and spatial omics data
Collection of analysis tools for quantitative trait loci
Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paper
Software implementing the Latent Causal Variable Model
A modular, high-performance computing solution to run jobs using SLURM
Tensors and Dynamic neural networks in Python with strong GPU acceleration
Fast, efficient RNA-Seq metrics for quality control and process optimization
dalmatian is a collection of high-level companion functions for Firecloud and FISS.
A deep learning-based tool to identify splice variants
requirements, examples, and tests for expression matrix file formats
A complete tool set for molecular QTL discovery and analysis
phasing and Allele Specific Expression from RNA-seq
Feather: fast, interoperable binary data frame storage for Python, R, and more powered by Apache Arrow
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")