Russel88's Stars
shap/shap
A game theoretic approach to explain the output of any machine learning model.
davidhalter/jedi-vim
Using the jedi autocompletion library for VIM.
andmarti1424/sc-im
sc-im - Spreadsheet Calculator Improvised -- An ncurses spreadsheet program for terminal
has2k1/plotnine
A Grammar of Graphics for Python
soedinglab/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
easystats/easystats
:milky_way: The R easystats-project
kblin/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
freebayes/freebayes
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
easystats/bayestestR
:ghost: Utilities for analyzing Bayesian models and posterior distributions
Ecogenomics/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
hyattpd/Prodigal
Prodigal Gene Prediction Software
easystats/correlation
:link: Methods for Correlation Analysis
rvlenth/emmeans
Estimated marginal means
glmmTMB/glmmTMB
glmmTMB
edgardomortiz/vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
adamkewley/jobson
A platform for transforming command-line applications into a job service.
RasmussenLab/vamb
Variational autoencoder for metagenomic binning
sanger-pathogens/snp-sites
Finds SNP sites from a multi-FASTA alignment file
cdanielmachado/carveme
CarveMe: genome-scale metabolic model reconstruction
AnantharamanLab/VIBRANT
Virus Identification By iteRative ANnoTation
medvedevgroup/SibeliaZ
A fast whole-genome aligner based on de Bruijn graphs
evolbioinfo/gotree
Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.
chrisquince/DESMAN
De novo Extraction of Strains from MetAgeNomes
cdanielmachado/smetana
SMETANA: a tool to analyse interactions in microbial communities
phiweger/nanotext
Proteins as words, genomes as documents.
arumugamlab/msamtools
Metagenomics-related extended functionalities to samtools
Wanli-HE/Plaspline
fabian-s/RLRsim
R package for fast & exact (restricted) likelihood ratio tests for mixed and additive models
pkerpedjiev/bwa-pssm
A burrows-wheeler transform-based probabilistic short read mapper.
eltanin4/trophic_gut
Scripts and data files relevant to the manuscript: "Evidence for a multi-level trophic organization of the human gut microbiome"