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koppsteinlab / cookiecutter-bioinformatics-project
Forked from maxplanck-ie/cookiecutter-bioinformatics-projectA 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
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Single-cell analysis in Python. Scales to >1M cells.
A Shiny web app for mapping datasets using Seurat v4
Awesome Image-based Phenotypic Drug Discovery 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
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.
A cross-platform command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, C projects.
A collection of resources for data scientists (not only) in bioinformatics