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Arkadiy-Garber

Arkadiy-Garber

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Company:Arizona State University

Location:Tempe, AZ

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Arkadiy-Garber's repositories

FeGenie

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

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SprayNPray

Rapid and simple taxonomic profiling of genome and metagenome contigs

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MagicLamp

A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.

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BagOfTricks

A collection of python and bash scripts for various bioinformatics-related tasks

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ParaHunter

Identification of gene paralogs in genomes, and calculation of dS and dN/dS values for paralogous gene pairs

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bvcn-binder-paml

Lesson and tutorial on generating codon alignments and estimating dN/dS using codeml (PAML)

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KOALA-formatter

Script for converting raw KO-number output from GhostKOALA and BlastKOALA into hierarchically-structured CSV format

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LithoGenie

HMM-based identification and categorization of genes and operons relevant to chemolithoautotrophic metabolisms

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Taxonsluice

Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables

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Middle-Author-Bioinformatics

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Arkadiy-Garber.github.io

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AstrobioMike.github.io

Site to help biologists wade their way into bioinformatics.

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binarena

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binder-variant-calling

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bioconda-recipes

Conda recipes for the bioconda channel.

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bioinf_tools

Bioinformatics Tools

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bvcn-binder-antismash

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bvcn-binder-htseq

Lesson and tutorial on generating count tables from read-mapping data

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bvcn-binder-lesson1

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bvcn-binder-magiclamp

Tutorial for the MagicCave toolkit

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bvcn-binder-pseudofinder

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bvcn-binder-trinity

Tutorial on transcriptome assembly using Trinity

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Coriolan

A lightweight software to generate phylogenomic trees from unannotated genomes

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MAB

Minima is a one-size-fits-all Jekyll theme for writers.

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MHCscan

Software tool for identification of multiheme cytochromes

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PLOS-Biology-Review-code

Custom scripts used for PLOS Biology Review

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PseudoHunter

Identification of pseudogenes based on pairwise comparison between genomes

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silvaMapper

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Supplement-for-Acaryochloris-Duplication-Paper

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Supplement-for-Garber2021-GBE

Python scripts used in the analysis of P. longispinus endosymbionts.

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