A Markdown browser for your terminal

A cookiecutter template for bioinformatics projects, inspired by cookiecutter-data-science and Snakemake Workflows.

The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized format

B-field implementation in Rust

Comparison of multiple long read datasets

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

The R Installation Manager

Single-cell analysis in Python. Scales to >1M cells.

A Shiny web app for mapping datasets using Seurat v4

tools and notes for spatial omics

Awesome Image-based Phenotypic Drug Discovery & Image-based Cell Profiling Papers and Codes

The CUBI's public knowledge base: a Wiki for how-to instructions, best practices and helpful hints

A massively parallel, high-level programming language

Collaborative Interpretation-Pipeline workflow based on nf-core pipeline structure

A curated list of Rust code and resources.

fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector

Syntax highlighting for computational biology

Workshops presented by the Gladstone Bioinformatics Core

Clair3-RNA - a long-read small variant caller for RNA sequencing data

Dataframes powered by a multithreaded, vectorized query engine, written in Rust

Simple pileup-based variant caller

Long read production pipelines

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

A curated list of awesome nanopore analysis tools.

minimal example implementations for bioinformatics workflow managers

🦀 Small exercises to get you used to reading and writing Rust code!

rattler-build is a universal package builder for Windows, macOS and Linux

Conda recipes for the bioconda channel.