17 best open source variants projects.

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Displaying 1 to 17 from 17 results

postcss-font-magician - Magically generate all the @font-face rules

Javascript

Font Magician is a PostCSS plugin that magically generates all of your @font-face rules. Never write a @font-face rule again. Just use the font and font-family properties as if they were magic.

postcss css postcss-plugin fonts faces generate generation weights styles variants typography type

go-feature-flag - A simple and complete feature flag solution, without any complex backend system to install, all you need is a file as your backend

A simple and complete feature flag solution, without any complex backend system to install, all you need is a file as your backend. No server is needed, just add a file to your central system and all your services will react to the changes in this file.

devops continuous-delivery continuous-deployment feature-flags feature-toggles variants continuous-testing toggles help-wanted golang-library experiments beginner-friendly feature-toggle feature-flag feature-toggling

indexed-string-variation - Experimental JavaScript module to generate all possible variations of strings over an alphabet using an n-ary virtual tree

Javascript

Experimental JavaScript module to generate all possible variations of strings over an alphabet using an n-ary virtual tree. Generally useful to create distributed brute-force password recovery tools or other software that might require distributed generation of all possible strings on a given alphabet.

alphabet tree algorithm virtual characters nodejs node library variations duplicates strings string javascript-library variation variants generator generation brute-force cracker n-ary

rvtests - Rare variant test software for next generation sequencing data

Rvtests, which stands for Rare Variant tests, is a flexible software package for genetic association analysis for sequence datasets. Since its inception, rvtests was developed as a comprehensive tool to support genetic association analysis and meta-analysis. It can analyze both unrelated individual and related (family-based) individuals for both quantitative and binary outcomes. It includes a variety of association tests (e.g. single variant score test, burden test, variable threshold test, SKAT test, fast linear mixed model score test). It takes VCF/BGEN/PLINK format as genotype input file and takes PLINK format phenotype file and covariate file. With new implementation of the BOLT-LMM/MINQUE algorithm as well as a series of software engineering optimizations, our software package is capable of analyzing datasets of up to 1,000,000 individuals in linear mixed models on a computer workstation, which makes our tool one of the very few options for analyzing large biobank scale datasets, such as UK Biobank. RVTESTS supports both single variant and gene-level tests. It also allows for highly effcient generation of covariance matrices between score statistics in RAREMETAL format, which can be used to support the next wave of meta-analysis that incorporates large biobank datasets.

next-generation-sequencing ngs association-analysis gwas rare-variant meta-analysis genotype skat c-plus-plus variants umich genetics kernel vcf-files

google-fonts-complete - A complete list of Google Web Fonts and their sources

Javascript

A complete list of Google Fonts and their sources. This list is generated from the Google Fonts API.

google web fonts complete families family styles variants weights

negotiate-js - A JavaScript implementation of proper HTTP content negotiation

Javascript

Negotiate.js is a JavaScript implementation of proper HTTP content negotiation, and is designed to be compatible with Node.js's HTTP Request API. Content negotiation is an optional feature of the HTTP protocol that allows for the automatic selection of the appropriate content representation of the requested resource based upon the attributes of the request and variants.

http content negotiation variants node accept

TeamTeri - Artifacts for the Cancer Genomics on GCP or AWS

Shell

Artifacts for patterns / tools for cloud-scaling cancer genomic data pipelines using... As with any genome sequencing project, the reads must be assembled to form a representation of the chromosomes being sequenced. With cancer genomes, this is usually done by aligning the reads to the human reference genome.

cancer-genomics variants genome-analysis genome-sequencing gcp aws variant-calls bioinformatics

ga4gh-server - Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Python

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

ga4gh genomics server global alliance health variants rna genome-annotation reference-implementation bioinformatics

gatk4-somatic-snvs-indels - Workflows for somatic short variant discovery with GATK4

Workflows for somatic short variant analysis with GATK4. Implements Somatic short variant discovery using GATK Best Practices. Note: Also provided in this repo is mutect2_nio which is a NIO supported version of the wdl.

mutect gatk tumor variants

civic-client - Web client for CIViC: Clinical Interpretations of Variants in Cancer

Javascript

Developing for CIViC involves setting up a development environment. To get started quickly, we recommend launching an AWS EC2 instance from our pre-configured and maintained AMI (getting started wiki page). Alternatively, you may set up your own local development environment using the following setup instructions.

nci-itcr civic front-end-framework cancer cancer-genomics variants

civic-server - Backend Server for CIViC Project

HTML

This repository contains the server component of the CIViC. It is a Ruby on Rails application that serves JSON data to power the frontend website and API. Developing for CIViC involves setting up a development environment.

nci-itcr civic backend-server cancer cancer-genomics variants

needlestack - Multi-sample somatic variant caller

Warning: development in progress, unreliable results warranted. Please wait upcoming publication before using it in production.

nextflow pipeline regression bam-files variants ngs somatic-mutations negative-binomial-regression samtools docker

maftools - Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widley accepted and used to store variants detected. The Cancer Genome Atlas Project has seqenced over 30 different cancers with sample size of each cancer type being over 200. The resulting data consisting of genetic variants is stored in the form of Mutation Annotation Format. This package attempts to summarize, analyze, annotate and visualize MAF files in an efficient manner either from TCGA sources or any in-house studies as long as the data is in MAF format. Maftools can also handle ICGC Simple Somatic Mutation format. Please cite the below if you find this tool useful for you.

maf-files cancer-genomics variants cancer-genome-atlas visualize-maf-files tcga

vcf.js - A VCF parser and variant record model in JavaScript.

Javascript

VCF.js is a library that can remotely load and parse VCF files, or JSON representations of them. It is used to manipulate and analyse genotype calls. Documentation can be found in DOCUMENTATION.md.

vcf bigdatagenomics genomics variant-calling variants

bamsplit - Split a BAM file by haplotype support

Python

bamsplit is a simple Python3 tool for splitting a SAM format file by reads supporting different haplotypes present in a phased VCF file. This can be useful for visualisation, but also for splicing variants into reads from a single haplotype. The tool takes a VCF file which contains variants present in an individual and a BAM file containing sequencing reads from the same individual. These reads may or may not be the ones used to call the input variants. The variants should be phased to the greatest extent possible as this improves read assignment accuracy. The tool then produces three new BAM files: two for reads supporting each haplotype in the sample, and a third for reads that cannot be assigned to a haplotype. An example input and output are shown below.

bam-files bioinformatics haplotypes variants

octopus - Bayesian haplotype-based mutation calling

Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time. Octopus calls SNVs, small-medium sized indels, and small complex rearrangements in VCF 4.3.

bioinformatics genomics somatic-variants haplotypes variants variant-calling single-cell phasing de-novo-mutation

rare-disease-wf - (WIP) best-practices workflow for rare disease

Nextflow

Note, it is early days for the project. It will produce high-quality SNP/indel candidates but you may need experience with nextflow to run it easily. See this wiki page for more information about how to use the output.

genomics variants rare-disease