kohei-108

kohei-108's Stars

• davidemms/OrthoFinder

  Phylogenetic orthology inference for comparative genomics

  Language:Python66627890185

• cxli233/Online_R_learning

  Online R learning for applied statistics

  47618397

• oschwengers/bakta

  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  Language:Python4251321749

• biobakery/MetaPhlAn

  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

  Language:Python2881920583

• widdowquinn/pyani

  Application and Python module for average nucleotide identity analyses of microbes.

  Language:Python1921125255

• AnantharamanLab/METABOLIC

  A scalable high-throughput metabolic and biogeochemical functional trait profiler

  Language:Perl170418242

• ctberthiaume/gdcp

  scp like tool to interact with Google Drive from the command-line

  Language:Python161213020

• ksahlin/strobealign

  Aligns short reads using dynamic seed size with strobemers

  Language:C++1351016917

• wwood/singlem

  Novelty-inclusive microbial community profiling of shotgun metagenomes

  Language:Python119913016

• phac-nml/mob-suite

  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

  Language:Python1151214231

• oschwengers/platon

  Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

  Language:Python10564215

• bokulich-lab/RESCRIPt

  REference Sequence annotation and CuRatIon Pipeline

  Language:Python88107726

• gtonkinhill/panstripe

  post processing of bacterial pangenome gene presence/absence matrices

  Language:R502156

• 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.

  Language:R4952011

• jlw-ecoevo/gRodon2

  Language:R363122

• ku-cbd/PhageBoost

  Rapid discovery of novel prophages using biological feature engineering and machine learning

  Language:Jupyter Notebook345296

• 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.

  Language:Python287125

• treangenlab/emu

  Language:Python275143

• KechrisLab/SmCCNet

  A canonical correlation analysis based method for discovering (quantitative) trait-specific heterogeneous regulatory networks.

  Language:R24615

• gauravsk/ranacapa

  R package for downstream analysis for anacapa eDNA pipeline

  Language:R2273311

• BioinfoHR/coRdon

  Codon Usage Analysis and Prediction of Gene Expressivity

  Language:R194171

• MrTomRod/scoary-2

  Calculate assocations between genes and traits

  Language:Python182131

• sxh1136/Phage_tools

  Phage prediction tools

  Language:Shell15221

• padpadpadpad/bartlett_et_al_2022_human_pathogens

  Language:HTML13402

• xiaole99/ARGs-OAP-v2.0-development

  This is the source code for ARGs-OAP v2.0 construction

  Language:Python12016

• ChaonanLi/microgeo

  Language:R61

• milnus/Corekaburra

  Program to find core gene consensus synteny, hotspots between these, and construct spatially aware multiple sequence alignments of core genes

  Language:Python5194

• smarini/AMR-meta

  kmer- and matrix-factorization-based classifier for metagenomics data

  Language:R52

• chan-csu/SPAM-DFBA

  Formal repository for "Microbial Interactions from a New Perspective: Reinforcement Learning Reveals New Insights into Microbiome Evolution"

  Language:HTML4204

• computational-nutrition-lab/DietDiveR

  DietR repo has been copied and renamed as DietDiveR.

  Language:R410