marianattestad Goto Github PK
Name: Maria Nattestad
Type: User
Bio: Creator of Circa, omgenomics.com. Ex-Google DeepVariant/DeepConsensus team. PhD in genomics from CSHL.
Twitter: marianattestad
Location: Mountain View, CA
Blog: omgenomics.com
Name: Maria Nattestad
Type: User
Bio: Creator of Circa, omgenomics.com. Ex-Google DeepVariant/DeepConsensus team. PhD in genomics from CSHL.
Twitter: marianattestad
Location: Mountain View, CA
Blog: omgenomics.com
Allows users to play with alignments and mess with the scoring matrix.
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
Deprecated in favor of main Assemblytics repo, containing both web and CLI versions.
A tutorial in Python where all the examples teach students about biology. Written for high school students with no previous experience.
A simple web application for teaching students about transcription and translation of DNA into RNA into protein.
Copycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV)
D3 plugin for doing live search using an input box and giving partial match suggestions which are selectable by click or arrow keys.
D3 plugin to make a table out of a list of objects. Includes examples.
Dot: An interactive dot plot viewer for comparative genomics
Three examples using FileReader to load and display the contents of a file, using 1) only javascript, 2) D3, and 3) JQuery.
A small example app showing gene search on a csv annotation file using D3.js
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
New static website for marianattestad.com
Primarily useful for plots with chromosomes displayed sequentially, such as Manhattan plots, circos plots, or in Dot. Acts like a regular scale but takes a key to a segment followed by the position within that segment and outputs a number for the relative position along the total length of that genome.
Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file
Replacing the wordpress site currently on omgenomics.com with this on GitHub pages.
A buffet of analysis scripts available after running Assemblytics
Scripts and data for Plotting in R for Biologists, a video course on YouTube
Code and example data from an R for biology workshop I taught at CSHL.
A genome browser designed for complex structural variants and long reads.
Explore rearrangements and copy-number amplifications in a cancer genome
Uses D3 to auto-generate UI elements based on a style schema
A template for building visualization tools
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.