machine-readable file format for genomic library sequence and structure
☆128Feb 9, 2026Updated 2 weeks ago
Alternatives and similar repositories for seqspec
Users that are interested in seqspec are comparing it to the libraries listed below
Sorting:
- Flexible and efficient parsing, interpreting and editing of sequencing reads☆45Dec 8, 2025Updated 2 months ago
- A pipeline creation tool using Snakemake☆12Feb 20, 2026Updated last week
- Context specific and dynamic gene regulatory network reconstruction and analysis☆127Nov 24, 2025Updated 3 months ago
- Rust UMI Directional Adjacency Deduplicator☆15Nov 25, 2019Updated 6 years ago
- Collections of library structure and sequence of popular single cell genomic methods☆494May 19, 2025Updated 9 months ago
- Location of public benchmarking; primarily final results☆18Feb 17, 2025Updated last year
- ☆20May 24, 2025Updated 9 months ago
- Repository for RecallME-v.0.1 a variant calling pipelines benchmarker and optimizer☆13Dec 18, 2023Updated 2 years ago
- Finding gene expression states in scRNA-seq data☆50Mar 22, 2024Updated last year
- An end-to-end computational pipeline for large Perturb-seq screens☆15Apr 25, 2025Updated 10 months ago
- overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites☆34Jun 6, 2025Updated 8 months ago
- A high-performance BigWig and BigBed library in Rust☆112Feb 13, 2026Updated 2 weeks ago
- A tool to find sequencing data and metadata from public databases.☆595Aug 13, 2024Updated last year
- Biological sequence analysis for the modern age.☆263Feb 22, 2026Updated last week
- genes and genomes at your fingertips☆407Sep 30, 2025Updated 5 months ago
- A flexible and extensible API for annotated 2D matrix data stored in multiple underlying formats.☆83Updated this week
- Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"☆21Nov 27, 2025Updated 3 months ago
- Bayesian analysis of MPRA and other high-throughput genomic assays☆10Jul 27, 2020Updated 5 years ago
- Fast FASTQ sample demultiplexing in Rust.☆67Feb 4, 2026Updated 3 weeks ago
- This tools counts the number of specific k-mers within sequence data. The counts can then be compare to other counts to determine to comp…☆30Nov 25, 2024Updated last year
- A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.☆65Apr 5, 2024Updated last year
- 🧬 gget enables efficient querying of genomic reference databases☆1,099Updated this week
- A set of tools for accurate quantitation of single-cell allele-specific expression☆13Dec 26, 2022Updated 3 years ago
- vcfdist: Accurately benchmarking phased variant calls☆84Updated this week
- Download FASTQ files from SRA or ENA repositories.☆369Feb 1, 2026Updated last month
- a minimal, scriptable genome browser for python☆53Dec 20, 2024Updated last year
- Single-cell epigenomics analysis tools☆309Feb 12, 2026Updated 2 weeks ago
- Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.☆122Updated this week
- long read RNA-seq quantification☆105Feb 4, 2026Updated 3 weeks ago
- Fast motif matching in R☆46Jan 24, 2024Updated 2 years ago
- Example genomics data for tool developers☆117Jul 7, 2024Updated last year
- Analysis Pipeline for Single Cell ATAC-seq☆321Apr 27, 2023Updated 2 years ago
- ☆13May 27, 2025Updated 9 months ago
- Tools for working with BUS files☆102May 27, 2025Updated 9 months ago
- Tool for plotting sequencing data along genomic coordinates.☆336Dec 12, 2025Updated 2 months ago
- Tools for processing UMI RNA-tag data☆131Mar 15, 2023Updated 2 years ago
- Formalizing and benchmarking open problems in single-cell genomics☆420Nov 26, 2025Updated 3 months ago
- vembrane filters VCF records using python expressions☆68Jan 8, 2026Updated last month
- Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq dat…☆15Apr 28, 2025Updated 10 months ago