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16s_analysis

A ruby implementation to digest both 454 amplicon outputs by MID, plus Ibis data

16s_classification

Takes output from the rdp (ribosomal database project) program and reports in excel sheets bacteria numbers from a sample by level of phylogenetic classification.

42_hihh_circos

add_user

Add a new user to the cluster

bac_classification

A ruby pipeline for the classification of 16s amplicon sequencing.

bam_error_analysis

Calculate position specific differences to the reference

calc_error_from_illumina_assembly

Use bwa, sambama to call variants and find error in an Illumina assembly

calc_pacbio_assembly_stats

script to calculate statistics from pacbio assemblies

calculate_divergence

Calculate the pairwise divergence of a sliding window over an MSA

camplim

Lims for Drexel CAMP

cluster_analysis

Bioruby program to analyze gene cluster (family) distributions in multi-genome comparisons

cluster_features

Ok, this time I'm really making a rails app

cluster_view

Rails app to examine clusters in a web interface

create_hap

Create input for orderedPainting program from fasta MSA

demo_app

Ruby On Rails demo application

depot

depot

dominion_database

Database to track the dominion games I've played

dot_files

My config files. Just the way I like them. Not how you like them. Unless you like them the way I like them.

explore_ghost_clusters

Clusters sometimes contain 'ghost' annotations, I want to get more information about them.

extract_core_from_mauve_align

Extract a concatenated "core" string of dna from a multiple sequence alignment out of Mauve

family_recipes

A RoR site to store our delightful family recipes.

first_app

The first App for the Ruby on Rails Tutorial

fsgm

Finite supragenome model from Justin and Robert

gene_clusters_as_genomes_added

Show changes to core and total gene clusters as genomes increase from a gene presence absence matrix

genome_comparison

First attempt at my genome comparison website.

genomics-database-test

a test website for the genomics website

genomics_tools

Tools for calculating various genomics data

get_gene_list_dna

Node app to download the dna sequence of a list of gene names

guerrero_data_analysis

Files I used when creating the guerrero data analysis

increase_genomes_iteratively

Project to create a histogram showing the changes to the core genome size as new genomes are included