skembel

LightGBM

A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM or MART) framework based on decision tree algorithms, used for ranking, classification and many other machine learning tasks.

stat_rethinking_2022

Statistical Rethinking course winter 2022

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

sinerider

💖 A game about love and graphing, built by teenagers.

NanoPlot

Plotting scripts for long read sequencing data

serratus

Ultra-deep search for novel viruses

vamb

Variational autoencoder for metagenomic binning

Perfect-bacterial-genome-tutorial

DeepVirFinder

Identifying viruses from metagenomic data by deep learning

dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

DeepMicrobes

DeepMicrobes: taxonomic classification for metagenomics with deep learning

flextaxd

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

sci-hub-injector

Adds SciHub links to popular publisher websites

partis

B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction

isONclust

De novo clustering of long transcript reads into genes

gtdb-taxdump

GTDB taxonomy taxdump files with trackable TaxIds

sepia

taxonomic classifier based on the kraken2 algorithms and more

genome-grist

map Illumina metagenomes to genomes!

minotourapp

Minotour API, web and client code

POMS

Phylogenetic Organization of Metagenomic Signals (POMS)

tiebrush

Summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)

tidyamplicons

Functions to manipulate and visualize microbial community data

phylomatic-ws

Improved web service for phylomatic

PhD-defence-questions

Questions asked in PhD defences

Kilpisjarvi-MAGs

phylomatic-awk

A CLI phylomatic written in Gawk

Caribou

Alignment-free bacterial identification and classification in metagenomics sequencing data using machine learning

PhyloPGM

PhyloPGM

methylo-phyllo-diversity

Fine-scale adaptations to environmental variation and growth strategies drive phyllosphere Methylobacterium diversity.

budworm_biogeo