Code for the book "Software Engineering for Data Scientists"

TCR and BCR assembly from RNA-seq data

pix2tex: Using a ViT to convert images of equations into LaTeX code.

Regression Modeling Strategies

Survival package for R

❗ This is a read-only mirror of the CRAN R package repository. glmnet — Lasso and Elastic-Net Regularized Generalized Linear Models. Homepage: https://glmnet.stanford.edu

Interactive roadmaps, guides and other educational content to help developers grow in their careers.

freeCodeCamp.org's open-source codebase and curriculum. Learn math, programming, and computer science for free.

Circular visualization in R

Python library for calling Cytoscape Automation via CyREST

Run cBioPortal using Docker Compose

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Introduction course to transcriptomics

VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications. Users simply …

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Call and score variants from WGS/WES of rare disease patients.

Project documentation with Markdown.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

cBioPortal for Cancer Genomics

A simple, yet elegant, HTTP library.

This is the development home of the workflow management system Snakemake. For general information, see

This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.

A complete pipeline for metagenomic analysis

ATLAS - Three commands to start analyzing your metagenome data