Arkadiy-Garber
Microbiology, bioinformatics, symbioses, oceanography, astrobiology/geobiology.
Arizona State UniversityTempe, AZ
Pinned Repositories
BagOfTricks
A collection of python and bash scripts for various bioinformatics-related tasks
bioinf_tools
Bioinformatics Tools
bvcn-binder-paml
Lesson and tutorial on generating codon alignments and estimating dN/dS using codeml (PAML)
FeGenie
HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
KOALA-formatter
Script for converting raw KO-number output from GhostKOALA and BlastKOALA into hierarchically-structured CSV format
LithoGenie
HMM-based identification and categorization of genes and operons relevant to chemolithoautotrophic metabolisms
MagicLamp
A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.
ParaHunter
Identification of gene paralogs in genomes, and calculation of dS and dN/dS values for paralogous gene pairs
SprayNPray
Rapid and simple taxonomic profiling of genome and metagenome contigs
Taxonsluice
Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables
Arkadiy-Garber's Repositories
Arkadiy-Garber/FeGenie
HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
Arkadiy-Garber/SprayNPray
Rapid and simple taxonomic profiling of genome and metagenome contigs
Arkadiy-Garber/MagicLamp
A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.
Arkadiy-Garber/BagOfTricks
A collection of python and bash scripts for various bioinformatics-related tasks
Arkadiy-Garber/ParaHunter
Identification of gene paralogs in genomes, and calculation of dS and dN/dS values for paralogous gene pairs
Arkadiy-Garber/bvcn-binder-paml
Lesson and tutorial on generating codon alignments and estimating dN/dS using codeml (PAML)
Arkadiy-Garber/KOALA-formatter
Script for converting raw KO-number output from GhostKOALA and BlastKOALA into hierarchically-structured CSV format
Arkadiy-Garber/LithoGenie
HMM-based identification and categorization of genes and operons relevant to chemolithoautotrophic metabolisms
Arkadiy-Garber/Taxonsluice
Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables
Arkadiy-Garber/bioinf_tools
Bioinformatics Tools
Arkadiy-Garber/Middle-Author-Bioinformatics
Arkadiy-Garber/Arkadiy-Garber.github.io
Arkadiy-Garber/AstrobioMike.github.io
Site to help biologists wade their way into bioinformatics.
Arkadiy-Garber/binarena
Arkadiy-Garber/binder-variant-calling
Arkadiy-Garber/bioconda-recipes
Conda recipes for the bioconda channel.
Arkadiy-Garber/bvcn-binder-antismash
Arkadiy-Garber/bvcn-binder-htseq
Lesson and tutorial on generating count tables from read-mapping data
Arkadiy-Garber/bvcn-binder-lesson1
Arkadiy-Garber/bvcn-binder-magiclamp
Tutorial for the MagicCave toolkit
Arkadiy-Garber/bvcn-binder-pseudofinder
Arkadiy-Garber/bvcn-binder-trinity
Tutorial on transcriptome assembly using Trinity
Arkadiy-Garber/Coriolan
A lightweight software to generate phylogenomic trees from unannotated genomes
Arkadiy-Garber/MAB
Minima is a one-size-fits-all Jekyll theme for writers.
Arkadiy-Garber/MHCscan
Software tool for identification of multiheme cytochromes
Arkadiy-Garber/PLOS-Biology-Review-code
Custom scripts used for PLOS Biology Review
Arkadiy-Garber/PseudoHunter
Identification of pseudogenes based on pairwise comparison between genomes
Arkadiy-Garber/silvaMapper
Arkadiy-Garber/Supplement-for-Acaryochloris-Duplication-Paper
Arkadiy-Garber/Supplement-for-Garber2021-GBE
Python scripts used in the analysis of P. longispinus endosymbionts.