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16s_comparison

Comparing environmental 16S sequences to sequences from isolates

alexcritschristoph.github.io

Github Pages personal site.

ancestral_reconstruction_endonucleases

angelo_biosynthetic_genes_analysis

A repository for sharing code and additional data involved in the analysis for the paper

bgcexpression

A repository for my 2018 ISME poster: "Metatranscriptomic expression patternsof biosynthetic genes in soil communities"

canvd

DV-IMPACT (CANVD) is an online resource assessing disease variant impacts on PPI networks

dnafeaturesviewer

Fork of DnaFeaturesViewer for visualizing operons and synteny

dv-impact

The DV-IMPACT database repo

filter_reads.py

Filters BAM files created by bowtie2 for better read mapping. Use for genomes from metagenomes.

gisaidscraper

Scrapes FASTA files from GISAID

mag-isolate-comparison

reproducible rebuttal of Garg et al. preprint

metamarkers

Super fast microbial taxonomic profiling and visualization of metagenome assemblies

microbialgenomicsscripts

A selection of short scripts for analyzing microbial genomes

microbiomepriorityeffects

mobile_element_integration_quantification

mzstats

statistical tools for analyzing Tandem MS2 spectra of complex biological samples

papergraph

Visualizing networks of research papers

polycharthtmlwidget

An HTML Widget wrapper for the Polychart library.

qiime16stutorial

A tutorial on methods of 16S analysis with QIIME 1

rcharts_d3_sankey

rCharts implementation of d3 sankey plugin

rpxsuite

Identifies and clusters marker genes to delineate species groups in metagenomes

sars-cov-2_evolution

sars_cov_2_inversion

Reproducible analyses for analyzing proposed rare genomic inversions in SARS-COV-2

sigma

new sigmajs

soil_popgen

Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes

strains_analysis

Code for analyzing population genomics in genome-resolved metagenomes

vrca

Identifying ViRal and Circular content in metAgenomes

wastewater_sarscov2

Bay Area wastewater Sars-CoV-2