Scientific Software
Updated 6 months ago

covtobed — Peer-reviewed • Rank 4.5 • Science 93%

covtobed: a simple and fast tool to extract coverage tracks from BAM files - Published in JOSS (2020)

Updated 6 months ago

bedops • Rank 11.9 • Science 54%

:microscope: BEDOPS: high-performance genomic feature operations

Updated 6 months ago

BEDMatrix • Rank 10.7 • Science 26%

A matrix-like wrapper around PLINK .bed files

Updated 5 months ago

https://github.com/alexpreynolds/soda • Rank 5.6 • Science 13%

Python-based UCSC genome browser snapshot-taker and gallery-maker

Updated 5 months ago

https://github.com/alejandrogzi/packbed • Science 13%

pack a .bed into overlapping components

Updated 5 months ago

https://github.com/alexpreynolds/sample • Science 13%

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Updated 5 months ago

https://github.com/cumbof/tcga2bed • Science 13%

The Cancer Genome Atlas Data Extraction and Conversion Tool

Updated 5 months ago

https://github.com/cumbof/opengdc • Science 39%

An open-source Java tool to automatically extract and convert all clinical and genomic data from the Genomic Data Commons to BED, GTF, CSV, and JSON format

Updated 6 months ago

bamtocov • Science 67%

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  

Updated 5 months ago

https://github.com/alejandrogzi/gxf2bed • Science 26%

fastest GTF/GFF-to-BED converter chilling around

Updated 5 months ago

https://github.com/cumbof/opengdc.py • Science 39%

Python implementation of the OpenGDC software https://github.com/cumbof/OpenGDC

Updated 5 months ago

https://github.com/alexpreynolds/cull-exemplars • Science 13%

Filter lower-scoring, neighboring genomic intervals within a specified distance

Updated 5 months ago

https://github.com/brentp/bedder-rs • Science 26%

an API for intersections of genomic data