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Differential expression of RNA-seq data using the negative binomial.

FastQC is a bioinformatics tool for quality control of high-throughput sequencing data.

Cutadapt cleans high-throughput sequencing data by removing unwanted sequences like adapters, primers, and poly-A tails.

Hifiasm is a bioinformatics tool for de novo genome assembly, producing accurate, haplotype-resolved assemblies.

Samtools is a suite of programs for interacting with high-throughput sequencing data, including htslib and bcftools.

Salmon is a bioinformatics tool used to accurately measure RNA molecule abundance in cells.

BWA-MEM is a bioinformatics tool that aligns DNA sequencing reads to a reference genome.

HTSeq is a Python package for high-throughput sequencing data analysis, used for read counting and data manipulation.

STAR aligner is a bioinformatics tool for mapping RNA sequencing reads to a reference genome.

CELLxGENE is an open source cell-resolution data publishing and exploratory analysis platform for cell and tissue functionality.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence.

Suite2P is an imaging processing pipeline for registration, cell detection, spike detection, and visualization of cells.

Kilosort is a MATLAB package for spike sorting electrophysiological data up to 1024 channels.

Phy is an interactive visualization and manual spike sorting of large-scale electrophysiological data.

Toolbox for large scale calcium imaging, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

CellProfiler is a software package for quantitative analysis of biological images.