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Search results for java genomics

52 search results found

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

Biojava ⭐ 564

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Cbioportal ⭐ 535

cBioPortal for Cancer Genomics

Jvarkit ⭐ 440

Java utilities for Bioinformatics

A Java API for high-throughput sequencing data (HTS) formats.

Rtg Tools ⭐ 260

RTG Tools: Utilities for accurate VCF comparison and manipulation

Intermine ⭐ 228

A powerful open source data warehouse system

Miso Lims ⭐ 214

MISO: An open-source LIMS for NGS sequencing centres

Artemis ⭐ 191

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Exomiser ⭐ 174

A Tool to Annotate and Prioritize Exome Variants

Opencga ⭐ 164

An Open Computational Genomics Analysis platform for big data genomics analysis. OpenCGA is not maintained and develop by its parent company Zetta Genomics. Please contact [email protected] for bug report and feature requests.

Hmftools ⭐ 163

Various algorithms for analysing genomics data

Cloud Pipeline ⭐ 137

Cloud agnostic genomics analysis, scientific computation and storage platform

Dnanalyzer ⭐ 122

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Biojava Tutorial ⭐ 111

📖📚An introductory tutorial for BioJava

Dockerflow ⭐ 90

Dockerflow is a workflow runner that uses Dataflow to run a series of tasks in Docker with the Pipelines API

Genomicsdb ⭐ 88

High performance data storage for importing, querying and transforming variants.

Liblevenshtein Java ⭐ 40

Various utilities regarding Levenshtein transducers. (Java)

Genome Nexus ⭐ 38

Backend server for Genome Nexus

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

Dataflow Java ⭐ 35

Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.

A library for manipulating bioinformatics sequencing formats in Apache Spark

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

EzAAI - High Throughput Prokaryotic AAI Calculator

Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

phenol: Phenotype ontology library

UFCG: Universal Fungal Core Genes

Genomics data re-analysis

Java Genomics Toolkit ⭐ 16

Collection of scripts for working with Wiggle files and analyzing sequencing data

Omicssuite.github.io ⭐ 15

OmicsSuite website for releasing new version.

Csbfinder ⭐ 15

A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes

Umap Java ⭐ 14

A Uniform Manifold Approximation and Projection (UMAP) library for Java, developed by Tag.bio in collaboration with Real Time Genomics.

Chia Pet_tool_v3 ⭐ 13

ChIA-PET, HiChIP, PLAC-Seq data analysis, with linker detection, linker filter, or restriction process for HiChIP, mapping, call cluster and visulization

Blastgraph ⭐ 13

BACNET is a Java based platform to develop website for multi-omics analysis

Compliance ⭐ 10

Compliance test suite for the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Python Library for data analysis based on GMQL

Gluetools ⭐ 9

An open, platform-independent software toolkit for storage and interpretation of sequence data, implemented in Java.

Sketching ⭐ 8

Analyzing sketching and sampling approaches for fast and accurate read classification

Consent Ontology ⭐ 7

Broad Institute Data Use Oversight System

Pathway visualization and analysis tool for Pathway Commons and other BioPAX data

Emr Hbase Sample ⭐ 7

sample genomics application for use with hbase and emr

QA pipeline based on BaseQA and designed for biomedical related QA problems, like TREC Genomics tasks.

iPat allows you to perform GWAS and GS with drags and clicks!

CrypDist is a blockchain based data distribution tool

Broad Institute Data Use Oversight System

A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments.

Multisearch ⭐ 7

This is a command-line program for searching text for multiple words (or phrases) in a single pass. The runtime is O(n + m + z), where n is the length of the searched text, m is the total length of all the words we are looking for, and z is the total number of occurrences of words we are looking for.

Eager Gui ⭐ 5

The EAGER Pipeline

Ncbi_august_hackathon_push_button_genomics_solution ⭐ 5

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