SegataLab/cFMD

Public repository for cFMD - curatedFoodMetagenomicData

Size: 2.5 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 0 - Forks: 0

SegataLab/cmseq

Set of utilities on sequences and BAM files

Language: Python - Size: 7.03 MB - Last synced: 17 days ago - Pushed: over 2 years ago - Stars: 24 - Forks: 9

SegataLab/lefse

Language: Python - Size: 264 KB - Last synced: 9 days ago - Pushed: 14 days ago - Stars: 70 - Forks: 45

SegataLab/viromedb

Scripts for the ViromeDB project

Language: Python - Size: 520 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

SegataLab/panphlan

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples

Language: Python - Size: 292 KB - Last synced: 8 days ago - Pushed: 8 months ago - Stars: 39 - Forks: 7

SegataLab/MASTER-WP5-pipelines

Language: Python - Size: 89.8 KB - Last synced: 29 days ago - Pushed: 5 months ago - Stars: 3 - Forks: 2

SegataLab/metamlst

MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.

Language: Python - Size: 1.54 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 13 - Forks: 0

SegataLab/preprocessing

Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination

Language: Python - Size: 104 KB - Last synced: 5 months ago - Pushed: 6 months ago - Stars: 7 - Forks: 1

SegataLab/repophlan

Language: Python - Size: 11.7 MB - Last synced: 8 months ago - Pushed: over 4 years ago - Stars: 4 - Forks: 2

SegataLab/pyphlan

Language: Python - Size: 116 KB - Last synced: 8 months ago - Pushed: over 4 years ago - Stars: 3 - Forks: 2

SegataLab/PanPhlAn_pangenome_exporter

Language: Python - Size: 67.4 KB - Last synced: 10 months ago - Pushed: about 2 years ago - Stars: 4 - Forks: 1

SegataLab/MetaRefSGB_reports

Language: Python - Size: 15 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

SegataLab/metaml

Language: Python - Size: 43.3 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 19 - Forks: 11

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

Language: Python - Size: 677 KB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 14 - Forks: 1

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.

Language: Python - Size: 258 KB - Last synced: 5 months ago - Pushed: over 1 year ago - Stars: 10 - Forks: 3

SegataLab/export2graphlan

Conversion software tool for producing both annotation and tree files for GraPhlAn

Language: Python - Size: 592 KB - Last synced: 15 days ago - Pushed: over 2 years ago - Stars: 8 - Forks: 6

SegataLab/MetaRefSGB

Language: Python - Size: 931 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

SegataLab/FMT_Meta_Machine_Learning

Language: R - Size: 40 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

SegataLab/metaclock

A python package for assisting to reconstruct time-tree at the strain level using contemporary and ancient metagenomes.

Language: Python - Size: 10.6 MB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

SegataLab/calculus_study_Lena_2021

This repo contains scripts for reproducing results reported in the calculus study, Lena et al., 2021

Language: Python - Size: 17.6 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

SegataLab/Msmithii_molecular_clocking

Code available for Marsha et al. 2021 - "Reconstruction of ancient microbial genomes from the human gut"

Language: Python - Size: 5.26 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

SegataLab/multidataset_machinelearning

Language: Python - Size: 1.06 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1