Awesome GitHub RepositoriesAnalysis Pipelines

Automated pipeline for RNA-seq analysis.

Command-line tool for querying genomic databases.

High-performance disk-backed streaming calculations for RNA and ATAC-seq.

Toolkit for manipulating aligned single-cell reads.

Infers clonal selection and fitness landscapes.

Automated pipeline from raw fastq to count matrix.

Processes high-dimensional readouts from cell experiments.

Identifies bifurcating developmental trajectories.

Visualization tool for developmental datasets.

Analyzes LINE-1 mRNA expression at single-locus resolution.

Quantifies transposable element expression.

Rapidly assesses cell type identity using gene sets.

Exploration of immune repertoires in single-cell data.

Multi-agent framework for accelerating scientific code on CPUs.

Visualization tool for large-scale high-dimensional datasets.

Phylogenetic analysis of single-cell cancer samples.

Estimates and compensates spillover noise in CyTOF data.

Separates reads based on barcode sequences.

Downstream analysis and visualization for cytometry data.

Fetches metadata for single-cell genomics datasets.