Pinned Repositories
empress
A fast and scalable phylogenetic tree viewer for microbiome data analysis
qurro
Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
airplanefood
what's the deal with differential abundance
mocha-headless-chrome
Run client-side mocha tests in the command line through headless Chrome.
poisson-cat
Compute poisson differentials based on categorical sample metadata
pyfastg
A minimal Python library for parsing SPAdes FASTG files
strainFlye
Pipeline for analyzing (rare) mutations in metagenome-assembled genomes
wotplot
Small Python library for creating and visualizing dot plot matrices
MetagenomeScope
Visualization tool for (meta)genome assembly graphs
fedarko's Repositories
fedarko/airplanefood
what's the deal with differential abundance
fedarko/mocha-headless-chrome
Run client-side mocha tests in the command line through headless Chrome.
fedarko/poisson-cat
Compute poisson differentials based on categorical sample metadata
fedarko/qeeseburger
A very-much-in-progress collection of scripts and utilities for time-series microbiome analyses
fedarko/ampliviz
Visualizes breakpoint graphs generated by AmpliconArchitect; simulates the effects of long read data on the graph
fedarko/AstrobioMike.github.io
Site to help biologists wade their way into bioinformatics.
fedarko/COGS220Project
Combined chronological visualizations of news articles and tweets
fedarko/colander
Estimating strain variation in metagenome assemblies
fedarko/cse210-project
fedarko/DEICODE
Robust Aitchison PCA from sparse count data
fedarko/docs
Source repository for https://docs.qiime2.org
fedarko/FEAST
Fast expectation maximization for microbial source tracking
fedarko/gneiss
compositional data analysis toolbox
fedarko/hartig-net
repo of blog style tutorials (some under construction), hopefully it creates some nice symbiosis
fedarko/igraph
Library for the analysis of networks
fedarko/labadmin
Administration website for the Knight Lab
fedarko/LabControl
lab manager for plate maps and sequence flows
fedarko/neoconverter
Parses "CSV for Excel" data files from the NASA Earth Observations website
fedarko/plink-182
CSE 284 (Spring 2020, UCSD) final project
fedarko/python-igraph
Python interface for igraph
fedarko/q2-aldex2
qiime2 plugin for aldex2 for differential abundance analysis
fedarko/q2-breakaway
QIIME2 plug-in for breakaway
fedarko/q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
fedarko/q2-taxa
fedarko/q2stats-workshops
Repository of qiime2 workshops to explore microbial ecology
fedarko/qiita
Qiita - A multi-omics databasing effort
fedarko/songbird
Vanilla regression methods for microbiome differential abundance analysis
fedarko/songbird-feedstock
A conda-smithy repository for songbird.
fedarko/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
fedarko/tools
A collection of notebooks, scripts, etc useful for microbiome analyses