A curated list of resources for using LLMs to develop more competitive grant applications.

RNAnue

Pairwise whole genome aligner

An Open Source project with everything you need to learn about Rust.

An ensemble structural variant calling pipeline driven by snakemake using multiple SV and CNV callers.

Reference-guided transcript discovery and quantification for long read RNA-Seq data

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Fast and accurate gene fusion detection from RNA-Seq data

Python package to read and write R RData and Rds files into/from pandas dataframes. No R or other external dependencies required.

Code at the speed of thought – Zed is a high-performance, multiplayer code editor from the creators of Atom and Tree-sitter.

Visual Studio Code

Vim-fork focused on extensibility and usability

GoogleTest - Google Testing and Mocking Framework

A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).

RNAswarm is a nextflow pipeline for differential RNA-RNA interaction analysis using RNA cross-linking methodologies

Snakemake-based computational workflow for neoantigen prediction from diverse sources

JSON for Modern C++

The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth information, variants and DNA Gene features

LongcallR is a small variant caller for single molecule long-read RNA-seq data

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical…

Julia tool for the analysis and visualization of RNA-seq experiments producing chimeric reads.

The user-friendly command line shell.

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

A template for your READMEs

Explainable AI for Bioinformatics