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alignment_sandbox

Allows users to play with alignments and mess with the scoring matrix.

assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

assemblytics_web

Deprecated in favor of main Assemblytics repo, containing both web and CLI versions.

biocoding_tutorial

A tutorial in Python where all the examples teach students about biology. Written for high school students with no previous experience.

central-dogma

A simple web application for teaching students about transcription and translation of DNA into RNA into protein.

clonal-deconvolution-from-copy-number

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)

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.

d3-supertable

D3 plugin to make a table out of a list of objects. Includes examples.

dot

Dot: An interactive dot plot viewer for comparative genomics

filereader_examples

Three examples using FileReader to load and display the contents of a file, using 1) only javascript, 2) D3, and 3) JQuery.

gene_search

A small example app showing gene search on a csv annotation file using D3.js

igv

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

marianattestad-com

New static website for marianattestad.com

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.

nchart

Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file

old_python_splitthreader

omgenomics-com

Replacing the wordpress site currently on omgenomics.com with this on GitHub pages.

pca-on-genotypes

post-assemblytics

A buffet of analysis scripts available after running Assemblytics

r_for_biologists

Scripts and data for Plotting in R for Biologists, a video course on YouTube

r_tutorials_and_tricks

Code and example data from an R for biology workshop I taught at CSHL.

ribbon

A genome browser that shows long reads and complex variants better

splitthreader

Explore rearrangements and copy-number amplifications in a cancer genome

superui

Uses D3 to auto-generate UI elements based on a style schema

vistooltemplate

A template for building visualization tools