MariaNattestad
Creator of Circa, omgenomics.com. Ex-Google DeepVariant/DeepConsensus team. PhD in genomics from CSHL.
GoogleMountain View, CA
Pinned Repositories
Assemblytics
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
BioCoding_Tutorial
A tutorial in Python where all the examples teach students about biology. Written for high school students with no previous experience.
copycat
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)
dot
Dot: An interactive dot plot viewer for comparative genomics
Nchart
Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file
pca-on-genotypes
R_for_biologists
Scripts and data for Plotting in R for Biologists, a video course on YouTube
Ribbon
A genome browser that shows long reads and complex variants better
SplitThreader
Explore rearrangements and copy-number amplifications in a cancer genome
VisToolTemplate
A template for building visualization tools
MariaNattestad's Repositories
MariaNattestad/Ribbon
A genome browser that shows long reads and complex variants better
MariaNattestad/Assemblytics
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
MariaNattestad/SplitThreader
Explore rearrangements and copy-number amplifications in a cancer genome
MariaNattestad/R_for_biologists
Scripts and data for Plotting in R for Biologists, a video course on YouTube
MariaNattestad/dot
Dot: An interactive dot plot viewer for comparative genomics
MariaNattestad/BioCoding_Tutorial
A tutorial in Python where all the examples teach students about biology. Written for high school students with no previous experience.
MariaNattestad/copycat
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)
MariaNattestad/pca-on-genotypes
MariaNattestad/Nchart
Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file
MariaNattestad/VisToolTemplate
A template for building visualization tools
MariaNattestad/alignment_sandbox
Allows users to play with alignments and mess with the scoring matrix.
MariaNattestad/omgenomics-com
Replacing the wordpress site currently on omgenomics.com with this on GitHub pages.
MariaNattestad/Assemblytics_web
Deprecated in favor of main Assemblytics repo, containing both web and CLI versions.
MariaNattestad/d3-superTable
D3 plugin to make a table out of a list of objects. Includes examples.
MariaNattestad/multisegmentScale
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.
MariaNattestad/post-Assemblytics
A buffet of analysis scripts available after running Assemblytics
MariaNattestad/R_Tutorials_and_Tricks
Code and example data from an R for biology workshop I taught at CSHL.
MariaNattestad/superUI
Uses D3 to auto-generate UI elements based on a style schema
MariaNattestad/gene_search
A small example app showing gene search on a csv annotation file using D3.js
MariaNattestad/Central-Dogma
A simple web application for teaching students about transcription and translation of DNA into RNA into protein.
MariaNattestad/clonal-deconvolution-from-copy-number
MariaNattestad/d3-livesearch
D3 plugin for doing live search using an input box and giving partial match suggestions which are selectable by click or arrow keys.
MariaNattestad/FileReader_examples
Three examples using FileReader to load and display the contents of a file, using 1) only javascript, 2) D3, and 3) JQuery.
MariaNattestad/igv
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
MariaNattestad/marianattestad-com
New static website for marianattestad.com
MariaNattestad/old_python_splitthreader