Pinned Repositories
brefito
Snakemake pipelines for assembling and annotating bacterial reference sequences
breseq
breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
breseq-gui
Electron GUI for breseq
brnaseq
Basic analysis of bacterial RNAseq data for differential gene expression
efm-calculator
Evolutionary Failure Mode Calculator
LTEE-Ecoli
Genomics resources for the Long-Term Evolution Experiment with E. coli
mutant-protein-stability
Modeling the effects of mutations in proteins using PyRosetta
ostir
Software for predicting translation initiation rates in bacteria
pLannotate
Webserver and command line tool for annotating engineered plasmids
tacobot
Slack bot for tracking taco points
Barrick Lab's Repositories
barricklab/breseq
breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
barricklab/LTEE-Ecoli
Genomics resources for the Long-Term Evolution Experiment with E. coli
barricklab/ostir
Software for predicting translation initiation rates in bacteria
barricklab/pLannotate
Webserver and command line tool for annotating engineered plasmids
barricklab/breseq-gui
Electron GUI for breseq
barricklab/brnaseq
Basic analysis of bacterial RNAseq data for differential gene expression
barricklab/efm-calculator
Evolutionary Failure Mode Calculator
barricklab/barricklab
General data analysis spreadsheets and scripts
barricklab/cryptkeeper
Tool for visualizing unintentional bacterial gene expression from a DNA sequence
barricklab/fitnessR
R package for calculating relative fitness from co-culture competition assays
barricklab/mAdCap-Seq
Scripts to analyze multiplex adaptome sequencing data
barricklab/nsAA-kit
Scripts for nsAA measurement kit
barricklab/promoter-calculator
barricklab/brefito
Snakemake pipelines for assembling and annotating bacterial reference sequences
barricklab/Abaylyi-EE
Acinetobacter baylyi ADP1 evolution and engineering
barricklab/barricklab_calendar
Google Calendar to Slack Daily Events
barricklab/bioconda-recipes
Conda recipes for the bioconda channel.
barricklab/breseq-ext-cnv
breseq copy number variation extension
barricklab/FragGeneScan
barricklab/FUGUES
Protocols for Functional Genomics using Engineered Symbionts (FUGUES)
barricklab/genomediff-python
GenomeDiff (*.gd) file parser for Python
barricklab/igem2019
Scripts and datasets for measuring BioBrick plasmid burden.
barricklab/igem2021
barricklab/LTEE-metagenomic
Time-resolved metagenomic sequencing of Lenski's long-term evolution experiment with Escherichia coli
barricklab/ND-Bartonella-EE
Code for analyzing mutations that evolved in Bartonella bacteria passaged through rodents in the laboratory.
barricklab/ND-Bartonella-SSR
barricklab/RhoTermPredict
barricklab/seabreeze
Seabreeze: an automated pipeline for structrual variant analysis of bacterial resequencing experiments
barricklab/teachPress
Fork of teachPress (course and publication management plugin for WordPress) with some customizations
barricklab/widespread-recurrent-part-variants
Analysis code for identifying genetic part variants in engineered plasmids