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.

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.

rvtests - Rare variant test software for next generation sequencing data

  •    C++

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.




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.

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.

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.


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

  •    wdl

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.

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.

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.

needlestack - Multi-sample somatic variant caller

  •    R

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

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

  •    R

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.

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.

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.

octopus - Bayesian haplotype-based mutation calling

  •    C++

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.

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.






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