Pinned Repositories
cFMD
Public repository for cFMD - curatedFoodMetagenomicData
cmseq
Set of utilities on sequences and BAM files
export2graphlan
Conversion software tool for producing both annotation and tree files for GraPhlAn
hclust2
Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.
lefse
metaml
metamlst
MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.
panphlan
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
preprocessing
Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination
viromeqc
ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichment score for each virome. The score is calculated with respect to the expected prokaryotic markers abundances in reference metagenomes
Segata Lab's Repositories
SegataLab/lefse
SegataLab/panphlan
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
SegataLab/cmseq
Set of utilities on sequences and BAM files
SegataLab/metaml
SegataLab/viromeqc
ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichment score for each virome. The score is calculated with respect to the expected prokaryotic markers abundances in reference metagenomes
SegataLab/cFMD
Public repository for cFMD - curatedFoodMetagenomicData
SegataLab/metamlst
MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.
SegataLab/hclust2
Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.
SegataLab/preprocessing
Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination
SegataLab/export2graphlan
Conversion software tool for producing both annotation and tree files for GraPhlAn
SegataLab/repophlan
SegataLab/PanPhlAn_pangenome_exporter
SegataLab/MASTER-WP5-pipelines
SegataLab/pyphlan
SegataLab/FMT_Meta_Machine_Learning
SegataLab/metaclock
A python package for assisting to reconstruct time-tree at the strain level using contemporary and ancient metagenomes.
SegataLab/MetaRefSGB
SegataLab/MetaRefSGB_reports
SegataLab/viromedb
Scripts for the ViromeDB project
SegataLab/calculus_study_Lena_2021
This repo contains scripts for reproducing results reported in the calculus study, Lena et al., 2021
SegataLab/diet_habits_microbiome_association
Repository with the command lines used to generate the microbiome meta-analyses and the microbiome machine learning in the vegetarian, vegan, omnivore diet comparison paper
SegataLab/inverse_var_weight
Object caller for stochastically dependent and independent effect-size and meta-analysis of correlations in Python
SegataLab/Msmithii_molecular_clocking
Code available for Marsha et al. 2021 - "Reconstruction of ancient microbial genomes from the human gut"
SegataLab/multidataset_machinelearning