OCRmyPDF adds an OCR text layer to scanned PDF files, allowing them to be searched

Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 500 universities from 70 countries including Stanford, MIT, Harvard, and Cambridge.

Project documentation with Markdown.

The source code that powers readthedocs.org

Pytorch implementation of convolutional neural network visualization techniques

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

LD Score Regression (LDSC)

Structural variation caller using third generation sequencing

Plot structural variant signals from many BAMs and CRAMs

An accurate GFF3/GTF lift over pipeline

Performant Pythonic GenomicRanges

Interactive 2D scatter plot widget for Jupyter Lab and Notebook. Scales to millions of points!

GTEx & TOPMed data production and analysis pipelines

Structural variant toolkit for VCFs

MRI brain extraction tool

normalize the intensities of various MR image modalities

Long read based human genomic structural variation detection with cuteSV

tools for adding mutations to existing .bam files, used for testing mutation callers

Full-Length Alternative Isoform analysis of RNA

Biological sequence analysis for the modern age.

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)

RNA-seq prediction with deep convolutional neural networks.

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

High-precision TE Annotator

Pipeline to convert a haploid assembly into diploid

tomato graph pangenome

MultiMAP for integration of single cell multi-omics

A tool for evaluate long-read de novo assembly results

Knowledge-primed neural networks