morgansobol

morgansobol's Stars

• RILAB/statements

  Successful Job Applications and Grants

  677681127

• gamcil/clinker

  Gene cluster comparison figure generator

  Language:Python519149069

• wilkox/gggenes

  ➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

  Language:R49367749

• cdanielmachado/carveme

  CarveMe: genome-scale metabolic model reconstruction

  Language:Python152718852

• jotech/gapseq

  Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

  Language:R1521019532

• marbl/parsnp

  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

  Language:C++1271213125

• willgearty/deeptime

  Plotting Tools for Anyone Working in Deep Time

  Language:R834628

• hzi-bifo/traitar

  From genomes to phenotypes: Traitar, the microbial trait analyzer

  Language:Python5611015

• gtonkinhill/panstripe

  post processing of bacterial pangenome gene presence/absence matrices

  Language:R512166

• Kalan-Lab/zol

  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

  Language:Python45254

• cultivarium/GenomeSPOT

  Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome

  Language:Jupyter Notebook34472

• bacteria-archaea-traits/bacteria-archaea-traits

  A synthesis of bacterial and archaeal phenotypic trait data

  Language:R306411

• ericgoolsby/Rphylopars

  Phylogenetic Comparative Tools for Missing Data and Within-Species Variation

  Language:R2882711

• tamascogustavo/chimera

  Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.

  Language:HTML17241

• d-mcgrath/MetaPathPredict

  A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes.

  Language:Python16651

• celinescornavacca/ecceTERA

  Language:C++11125

• statdivlab/happi

  A Hierarchical Approach to Pangenomics Inference

  Language:R114294

• almlab/angst

  Analyzer of Gene and Species Trees

  Language:Python10855

• jrcasey/PanGEM

  Pangenome-scale metabolic network reconstruction, analysis, and strain-model extraction

  Language:MATLAB7103

• waglecn/GPA_evolution

  Associated files for Waglechner et al GPA evolution

  Language:UnrealScript4102

• WoldringLabMSU/AP-LASR

  Language:Python4104

• jrcasey/NutrientUptake

  Accompanying code to Casey and Follows, 2020. A flexible and easy-to-use model of microbial acclimation to nutrient availability.

  Language:MATLAB3100

• satellite830/AnnoView

  Workflow for AnnoView upload

  Language:Python3100

• wildberry93/oxyphen

  Program for oxygen phenotype assignment based on proteome sequences

  Language:Python3230

• jvollme/PO_2_GENECONTENT

  Generate GeneContent trees based on based the presence or absence of Genes from a given bacterial pan-genome using bidirectional BLAST results obtained with proteinortho

  Language:Python2300

• lucaz88/genome_comparison_code

  Companion repository to the article: "Comparative whole-genome approach to identify bacterial traits for microbial interactions"

  Language:R2110

• OSGConnect/tutorial-bwa

  Language:Shell2804

• PaulaRS/ProcessCount

  Prints total gene presences, multi, gains, losses, expansions, contractions per branch/node in the phylogenetic tree resulting from the Count software

  Language:Python2201

• carleton-spacehogs/sulfur

  A repository for scripts used in the analysis for the manuscript entitled "The evolution and spread of sulfur-cycling enzymes reflect volcanic sulfur sources and the redox state of the early Earth"

  Language:Python1010

• danbjensen/Oxygen_requirement_prediction

  Python scripts made to help predict bacterial oxygen requirements based on proteome composition

  1102