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antarctic_ha

Scripts supporting antarctic lake manuscript in development

bcubed

bcubed and weighted bcubed external validation index

bgreat

de Bruijn Graph REAd mapping Tool

bin3c

Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.

bio_corex

A flexible version of CorEx developed for bio-data challenges that handles missing data, continuous/discrete variables, multi-CPU, overlapping structure, and includes visualizations

bioconda-recipes

Conda recipes for the bioconda channel.

cat

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

cerebis.github.io

A repository for thoughts and ideas related primarily to my reseach interests in microbial genomics and metagenomics, community structure analysis, programming, scientific computing.

crblh

Protein homolog prediction by clustered reciprocal best LAST hit.

deap

Distributed Evolutionary Algorithms in Python

deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

deepvirfinder

Identifying viruses from metagenomic data by deep learning

docs

dram

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

freehic

FreeHi-C pipeline for high fidelity Hi-C data simulation.

gaml

Genome assembly by maximum likelihood

genomics_notes

A collection of scripts and notes related to genomics and bioinformatics

gfa_io

A simple module for reading GFA v1 files.

gi2020_poster

Genome Informatics 2020 Poster

graal

Software from Marie-Nelly et al., 2014 (High-quality genome assembly using chromosomal contact data)

graphbin2

GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

graphplas

GraphPlas: Assembly Graph Assisted Recovery of Plasmidic Contigs from TGS Assemblies

gtdbtk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

hic-box

hicseg

:exclamation: This is a read-only mirror of the CRAN R package repository. HiCseg — Detection of domains in HiC data

hiczin

HiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression

i3seqdb

Tracking and workflow instrumentation for NGS

idba-fork

Local fork

jellyfish

A fast multi-threaded k-mer counter

jellyfish_conda

Jellyfish k-mer counter conda packaging