kohei-108's Stars
davidemms/OrthoFinder
Phylogenetic orthology inference for comparative genomics
cxli233/Online_R_learning
Online R learning for applied statistics
oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
biobakery/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
widdowquinn/pyani
Application and Python module for average nucleotide identity analyses of microbes.
AnantharamanLab/METABOLIC
A scalable high-throughput metabolic and biogeochemical functional trait profiler
ctberthiaume/gdcp
scp like tool to interact with Google Drive from the command-line
ksahlin/strobealign
Aligns short reads using dynamic seed size with strobemers
wwood/singlem
Novelty-inclusive microbial community profiling of shotgun metagenomes
phac-nml/mob-suite
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
oschwengers/platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
bokulich-lab/RESCRIPt
REference Sequence annotation and CuRatIon Pipeline
gtonkinhill/panstripe
post processing of bacterial pangenome gene presence/absence matrices
KarstensLab/microshades
This repo contains the R microshades package, which contains a color blind accessible color palette with 30 unique colors and functions for applying these colors to microbiome data.
jlw-ecoevo/gRodon2
ku-cbd/PhageBoost
Rapid discovery of novel prophages using biological feature engineering and machine learning
biobakery/shortbred
ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.
treangenlab/emu
KechrisLab/SmCCNet
A canonical correlation analysis based method for discovering (quantitative) trait-specific heterogeneous regulatory networks.
gauravsk/ranacapa
R package for downstream analysis for anacapa eDNA pipeline
BioinfoHR/coRdon
Codon Usage Analysis and Prediction of Gene Expressivity
MrTomRod/scoary-2
Calculate assocations between genes and traits
sxh1136/Phage_tools
Phage prediction tools
padpadpadpad/bartlett_et_al_2022_human_pathogens
xiaole99/ARGs-OAP-v2.0-development
This is the source code for ARGs-OAP v2.0 construction
ChaonanLi/microgeo
milnus/Corekaburra
Program to find core gene consensus synteny, hotspots between these, and construct spatially aware multiple sequence alignments of core genes
smarini/AMR-meta
kmer- and matrix-factorization-based classifier for metagenomics data
chan-csu/SPAM-DFBA
Formal repository for "Microbial Interactions from a New Perspective: Reinforcement Learning Reveals New Insights into Microbiome Evolution"
computational-nutrition-lab/DietDiveR
DietR repo has been copied and renamed as DietDiveR.