BIFO

Alice McHardy's lab @ HZI

Braunschweig, Germany

Pinned Repositories

epitope-prediction
Language:Python15 6 511
epitope-prediction-paper
Data and results for the EpitopeVec paper
Language:Python5 5 03
Haploflow
Language:C++25 5 173
OligoMM
Scripts to reproduce analysis for Brugiroux et al. manuscript
Language:R4 5 00
Phylogeography_Paper
This repository contains all data and code for the manuscript "Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic".
Language:R6 8 21
Predicting_PA_AMR_paper
Language:Python5 25 02
Quasimodo
QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture
Language:C++13 6 103
RiboDetector
Accurate and rapid RiboRNA sequences Detector based on deep learning
Language:Python96 6 5416
seq2geno2pheno
5 6 44
traitar
From genomes to phenotypes: Traitar, the microbial trait analyzer
Language:Python56 11 015

BIFO's Repositories

hzi-bifo/RiboDetector
Accurate and rapid RiboRNA sequences Detector based on deep learning
Language:Python96 6 5416
hzi-bifo/Haploflow
Language:C++25 5 173
hzi-bifo/epitope-prediction
Language:Python15 6 511
hzi-bifo/Quasimodo
QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture
Language:C++13 6 103
hzi-bifo/epitope-prediction-paper
Data and results for the EpitopeVec paper
Language:Python5 5 03
hzi-bifo/AMR_benchmarking
Language:Python3 6 0
hzi-bifo/covid-germany-mcmc
SARS-CoV-2 lineage importations and spread are reduced after nonpharmaceutical interventions in phylogeographic analyses
Language:HTML2 5 0
hzi-bifo/scelestial-paper-materials-devel
The lineage tree reconstruction method based on Steiner tree problem - dataset and test scripts for the paper (development version)
Language:C++2 5 01
hzi-bifo/seq2geno
Reproducible and comprehensive sequence analyses for single-species bacterial dataset
Language:Tcl2 1 02
hzi-bifo/ChemLM
Language:Python1 6 00
hzi-bifo/corona_lineage_dynamics
SDPlots scripts for the coverage server
Language:C++1 5 20
hzi-bifo/mag
Best practice pipeline for assembly and binning of metagenomes based on CAMI2 challenge, adapted from nf-core/mag
Language:Nextflow1 0 2
hzi-bifo/Roary
Rapid large-scale prokaryote pan genome analysis
Language:Perl1 5 0
hzi-bifo/hcv-mds
Neutralization maps for HCV data
Language:Python0 5 40
hzi-bifo/AMR_prediction_pipeline
Language:Python5 0
hzi-bifo/AntigenicTreeTools
Language:Java
hzi-bifo/Broker4Microbiota
Django App for collection and storage of sequencing orders for the sequencing facility
Language:JavaScript1 6
hzi-bifo/corona_protein_dynamics
Mutation dynamics analysis of SARS-Cov-2 S-protein based on phylogenetics and statistics
Language:Python6 0
hzi-bifo/covid-germany-mcmc-one-tree-public
Language:R4 0
hzi-bifo/covid-germany-mcmc-phylogeo-tools
A phylogeo-tools for covid-germany-mcmc
Language:C++4 0
hzi-bifo/fastml
A copy of https://github.com/AidanDelaney/fastml with errors fixed
Language:C++
hzi-bifo/Haploflow_supplementary
Helper scripts and other supplementary material for Haploflow
Language:Python6 1
hzi-bifo/lotus
Scripts related to the Lotus japonicus root microbiota manuscript Zgadzaj, Garrido-Oter et al., 2016
Language:R5 0
hzi-bifo/ngs_form
Language:HTML4 0
hzi-bifo/phylogeny-of-single-cells
snakemake workflow for the phylogenetic reconstruction of single cell lineages from multiple displacement amplified single cell DNAseq
Language:Python6 01
hzi-bifo/sankoff
Language:C++5 0
hzi-bifo/scelestial
4 0
hzi-bifo/snakemake-workflow-univec-removal
A small Snakemake workflow to remove contaminating vector sequences from raw sequencing data using UniVec.
Language:Python6 0
hzi-bifo/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun metagenomic data
Language:Nextflow0 0
hzi-bifo/which_tree
Testing of phylogenetic inference methods
Language:R1 0