Nextflow pipeline to re-process all public single-cell RNA-seq data
☆31Jul 9, 2025Updated 7 months ago
Alternatives and similar repositories for scRecounter
Users that are interested in scRecounter are comparing it to the libraries listed below
Sorting:
- ☆19Feb 18, 2026Updated last week
- parallel differential expression for single-cell perturbation sequencing☆24Jan 7, 2026Updated last month
- Convert TCR gene names☆15Dec 26, 2025Updated 2 months ago
- LLM agents for working with the SRA and associated bioinformatics databases.☆153Nov 13, 2025Updated 3 months ago
- A simple, intuitive and Efficient single cell binary Data Storage format☆15Oct 10, 2019Updated 6 years ago
- Weakly supervised learning uncovers phenotypic signatures in single-cell data☆38Dec 17, 2025Updated 2 months ago
- Store collections of experimental data based on TileDB☆12Feb 16, 2026Updated last week
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- R interface to 'Gos'☆39Feb 23, 2023Updated 3 years ago
- MorphoDiff is a diffusion based generative pipeline to predict high-resolution cell morphological responses under different conditions ba…☆33Aug 13, 2025Updated 6 months ago
- Everything but the kitchen sink☆12Feb 6, 2025Updated last year
- ☆13Nov 15, 2017Updated 8 years ago
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 2025Updated 8 months ago
- Faster manipulation of dendrogram objects in R.☆15May 22, 2015Updated 10 years ago
- WebGL Renderer extension for Vega☆13Dec 10, 2021Updated 4 years ago
- R/Bioconductor package to interactively explore single cell clusters at multiple resolutions☆10Mar 10, 2022Updated 3 years ago
- Simple Jupyter chat UI for LangChain☆11Jul 3, 2024Updated last year
- Interactive package for Short AsyNchronous Time-series Analysis (SANTA) in R, implemented in Shiny☆11Mar 6, 2024Updated last year
- ☆11Sep 7, 2023Updated 2 years ago
- Annotate 2D point clouds using overlay polygons☆15Jun 19, 2025Updated 8 months ago
- Genomic Visualization Catalog☆13Oct 6, 2022Updated 3 years ago
- integrative pathway analysis with modern PCA methodology and gene selection☆11Jun 29, 2023Updated 2 years ago
- Reproducible GSEA Benchmarking☆14Oct 30, 2025Updated 4 months ago
- SIGnature is a Python package that empowers researchers to rapidly query gene sets across diverse single-cell RNA sequencing (scRNA-seq) …☆23Dec 12, 2025Updated 2 months ago
- String algorithm visualizations☆13Feb 7, 2023Updated 3 years ago
- Blacktie: a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline☆26Oct 5, 2015Updated 10 years ago
- Library to extract embeddings for DNA sequences using BioFM genomics foundation model☆19Aug 13, 2025Updated 6 months ago
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆28Feb 21, 2023Updated 3 years ago
- ☆25Feb 2, 2024Updated 2 years ago
- Squirreling Async SQL Engine☆30Feb 20, 2026Updated last week
- Index and query k-mer matrices in BGZF☆12Apr 30, 2018Updated 7 years ago
- Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.☆17Feb 11, 2026Updated 2 weeks ago
- Interactive visual analytic tool for exploring epigenomics data w/ associated metadata, powered by HiGlass and Gosling☆13Nov 10, 2023Updated 2 years ago
- Python Primer Design Library☆14Nov 24, 2025Updated 3 months ago
- A python package for chromVAR☆33May 1, 2023Updated 2 years ago
- cell type specific, trait-associated gene regulation☆29Mar 31, 2025Updated 11 months ago
- Introduction to Computational Biology☆33Nov 15, 2024Updated last year
- A performant scientific image visualization system.☆36Updated this week
- ☆59Jan 9, 2026Updated last month