alexcritschristoph
Making open source tools for microbiology
Johns Hopkins School of Public HealthBaltimore, MD
Pinned Repositories
mag-isolate-comparison
reproducible rebuttal of Garg et al. preprint
MicrobialGenomicsScripts
A selection of short scripts for analyzing microbial genomes
Qiime16sTutorial
A tutorial on methods of 16S analysis with QIIME 1
sars_cov_2_inversion
Reproducible analyses for analyzing proposed rare genomic inversions in SARS-COV-2
soil_popgen
Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes
VRCA
Identifying ViRal and Circular content in metAgenomes
wastewater_sarscov2
Bay Area wastewater Sars-CoV-2
MicrobeMod
A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
ORI-marker-screen
Software and Data for reproducible analysis for identifying functional origins in a pooled ORI-marker screen
inStrain
Bioinformatics program inStrain
alexcritschristoph's Repositories
alexcritschristoph/Qiime16sTutorial
A tutorial on methods of 16S analysis with QIIME 1
alexcritschristoph/MicrobialGenomicsScripts
A selection of short scripts for analyzing microbial genomes
alexcritschristoph/soil_popgen
Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes
alexcritschristoph/VRCA
Identifying ViRal and Circular content in metAgenomes
alexcritschristoph/wastewater_sarscov2
Bay Area wastewater Sars-CoV-2
alexcritschristoph/sars_cov_2_inversion
Reproducible analyses for analyzing proposed rare genomic inversions in SARS-COV-2
alexcritschristoph/mag-isolate-comparison
reproducible rebuttal of Garg et al. preprint
alexcritschristoph/angelo_biosynthetic_genes_analysis
A repository for sharing code and additional data involved in the analysis for the paper
alexcritschristoph/PaperGraph
Visualizing networks of research papers
alexcritschristoph/RPxSuite
Identifies and clusters marker genes to delineate species groups in metagenomes
alexcritschristoph/CANVD
DV-IMPACT (CANVD) is an online resource assessing disease variant impacts on PPI networks
alexcritschristoph/MetaMarkers
Super fast microbial taxonomic profiling and visualization of metagenome assemblies
alexcritschristoph/strains_analysis
Code for analyzing population genomics in genome-resolved metagenomes
alexcritschristoph/ancestral_reconstruction_endonucleases
alexcritschristoph/filter_reads.py
Filters BAM files created by bowtie2 for better read mapping. Use for genomes from metagenomes.
alexcritschristoph/mobile_element_integration_quantification
alexcritschristoph/SARS-CoV-2_Evolution
alexcritschristoph/16s_comparison
Comparing environmental 16S sequences to sequences from isolates
alexcritschristoph/alexcritschristoph.github.io
Github Pages personal site.
alexcritschristoph/BGCexpression
A repository for my 2018 ISME poster: "Metatranscriptomic expression patternsof biosynthetic genes in soil communities"
alexcritschristoph/DnaFeaturesViewer
Fork of DnaFeaturesViewer for visualizing operons and synteny
alexcritschristoph/DV-IMPACT
The DV-IMPACT database repo
alexcritschristoph/GISAIDScraper
Scrapes FASTA files from GISAID
alexcritschristoph/microbiomepriorityeffects
alexcritschristoph/mzStats
statistical tools for analyzing Tandem MS2 spectra of complex biological samples
alexcritschristoph/PolychartHTMLWidget
An HTML Widget wrapper for the Polychart library.
alexcritschristoph/rCharts_d3_sankey
rCharts implementation of d3 sankey plugin
alexcritschristoph/sigma
new sigmajs