jvineis Goto Github PK

anvio

An analysis and visualization platform for 'omics data

dada2-for-you

Reinventing the wheel of DADA2 analysis yet again

deep-core

Analysis of Metagenomic Data from four salt marsh sediment samples.

deep-core-cazyme-analysis

Analysis of short metagenomic sequencing reads for carbohydrate utilization

eemb1105-fish-coi

Tutorial to analyze COI DNA sequences of fish tissue collected from commercial and restaurant sources

enrichment-traps

functional_gene_db

Steps to create a fasta file of functional genes from 6000 ncbi "Gold" genomes and 8000 genomes derived from https://www.nature.com/articles/s41564-017-0012-7.

general-18s-processing

The scripts and notes regarding 18S amplicon sequencing analysis from TARA oceans and elsewhere

get-genomes-from-ncbi

A tutorial detailing how to download fasta files for a collection of genomes

get-jgi-data

A tutorial describing how to download data from a metagenomic project from jgi

get-ncbi-genomes

A tutorial that details how to download a list of genomes contained in the ncbi database

hbcf

Haplotype Based Conversion Finder for working with Adineta vaga genome and transcriptome

jgi-single-cell

A lab book for analysis of jgi single cell genomics

jvineis.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

mag-relative-abundance

Steps to calculate relative abundance of MAGs derived from separate assemblies across samples

marker-gene-analysis

The baby scripts and steps used to filter reads, assign taxonomy, analyze phylogeny, and visualize: nrfA, nirS, dsrB

med-anvio-workshop

A collection of information for how to use MED and anvio with fun examples and some discussion. Both the Anvio and MED have their own tutorial pages which are far more in depth and informative but this page contains information relevant to a workshop hosted at Northeastern University Marine Resource Center.

mesocosm_18s

mesocosm_metag

The steps and scripts that I used to analyze the MOSS Landing metagenomic data including both prokaryotic and eukaryotic lineages -- functions abundance and beyond

mg_rast_processing

Sick of struggling with the MG-RAST website and can't get the API to do what you are asking. Here is a step by step process to pull the data that you want from MG-RAST

my_sequence_utilities

scripts for dealing with sequence data primarily from illumina sequencing platforms

nitrate-enrich-short-read

The steps taken to analyze the short reads generated by JGI for the PIE LTER fertilization experiment.

reactor-metagen

The steps required to repeat bioinformatic analysis used in the manuscript "Microbial dark carbon fixation fueled by nitrate enrichment"

swarm-analysis

symmf_net

Microbiome network analysis

tara-18s