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andreasprlic.github.io

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anyvar

[in development] Proof-of-Concept variation translation, validation, and registration service

biocommons.seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

biojava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

biojava-http

HTML/JS based user interfaces for BioJava

biojava-legacy

Legacy BioJava 1 Code

biojava-spark

:collision: Algorithms that are built around BioJava and run on Apache Spark

biojava3-tutorial

A tutorial for BioJava 3

bioutils

bioutils provides some common tools and lookup tables used primarly by the hgvs and uta packages

dalliance

Interactive web-based genome browser.

eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

karyotypesvg

A javascript library to generate SVG based ideograms of chromosomes showing cytogenetic bands

kaviar_mapping

logo

A repository to host the competition for a new BioJava log

mediawiki_to_git_md

Convert a MediaWiki export XML file into MarkDown as a series of git commits

mirrors-ncbi

mmtf-java

The java implementation of the MMTF API, decoder and encoder.

mmtf-spark

A module to hold Spark examples and functions for the MMTF project

ngl

WebGL protein viewer

pdbdistances

Find proteins by the distances between their atoms.

protein-project

proteinfeatureview

The Protein Feature View - a SVG library for visualising protein annotations

pv

WebGL protein viewer

quickstructuresearch

Methods for fast structural database searches and clustering

rcsb-sequenceviewer

PDB Amino Acid Sequence Viewer

rcsb-viewers

Biojava based RCSB Viewers

sisyphus

An archive of data for the legacy Sisyphus project

snpsinpdb

supplemental material for a manuscript that is under review