COMBINE-lab / alevin-fryView external linksLinks
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
☆200Jan 27, 2026Updated 2 weeks ago
Alternatives and similar repositories for alevin-fry
Users that are interested in alevin-fry are comparing it to the libraries listed below
Sorting:
- A rust framework to make using alevin-fry even simpler☆62Apr 29, 2025Updated 9 months ago
- Tools for working FASTQ files from sequencers (R1/R2/I1/I2)☆12Dec 6, 2024Updated last year
- ☆16Jan 6, 2025Updated last year
- ☆57Aug 11, 2022Updated 3 years ago
- Rust wrapper for the next generation (still currently in C++)☆30Feb 8, 2026Updated last week
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆859May 29, 2024Updated last year
- ☆19Jan 24, 2025Updated last year
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 years ago
- Differential expression and allelic analysis, nonparametric statistics☆30Jan 3, 2025Updated last year
- A tool for semi-automatic cell type classification☆451Jan 31, 2026Updated 2 weeks ago
- 10x Genomics Single Cell Analysis☆444Dec 10, 2025Updated 2 months ago
- Clustering scRNAseq by genotypes☆193Nov 11, 2025Updated 3 months ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆179Mar 27, 2025Updated 10 months ago
- Single-cell epigenomics analysis tools☆308Feb 1, 2026Updated 2 weeks ago
- Fast FASTX parsing and k-mer methods in Rust☆209Jan 27, 2026Updated 2 weeks ago
- This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.☆353Jan 29, 2026Updated 2 weeks ago
- Reference mapping for single-cell genomics☆398Dec 2, 2025Updated 2 months ago
- A Rust library and command line tool for working with genomic ranges and their data.☆101May 29, 2024Updated last year
- Bioinformatics I/O libraries in Rust☆650Feb 8, 2026Updated last week
- An efficient CLI to extract sequences from the SRA☆120Jan 30, 2026Updated 2 weeks ago
- Singular Genomics Demultiplexing Tool☆16Mar 5, 2024Updated last year
- This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementat…☆1,774Feb 9, 2026Updated last week
- R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the …☆121Dec 5, 2025Updated 2 months ago
- Tools for working with BUS files☆102May 27, 2025Updated 8 months ago
- CellRank: dynamics from multi-view single-cell data☆427Updated this week
- An efficient index for the colored, compacted, de Bruijn graph☆111Oct 7, 2024Updated last year
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆312Nov 1, 2022Updated 3 years ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,345Updated this week
- ☆21Dec 26, 2025Updated last month
- Rust wrapper for STAR aligner☆19Updated this week
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆245Jan 16, 2026Updated 3 weeks ago
- A high-performance BigWig and BigBed library in Rust☆113Oct 21, 2025Updated 3 months ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆490Feb 7, 2026Updated last week
- long read RNA-seq quantification☆102Feb 4, 2026Updated last week
- Simple and transparent support for compressed files.☆81Feb 12, 2025Updated last year
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆376Jul 30, 2025Updated 6 months ago
- Convert between AnnData and SingleCellExperiment☆143Updated this week
- Aligning gene expression trajectories of single-cell reference and query systems☆81Aug 10, 2025Updated 6 months ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,563Updated this week