-
proxigenomics_toolkit Public
A collection of classes and methods for the analysis of 3C-based sequencing data.
Python GNU Affero General Public License v3.0 UpdatedSep 16, 2025 -
bin3C Public
Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.
-
gfa_io Public
A simple module for reading GFA v1 files.
-
seq_embed Public
Calculate chunked embeddings for a set of DNA sequences using DNABERT-S.
Python GNU General Public License v3.0 UpdatedApr 1, 2025 -
-
shap Public
Simple High-throughput Annotation Pipeline
Java GNU General Public License v3.0 UpdatedAug 24, 2024 -
emg-viral-pipeline Public
Forked from EBI-Metagenomics/emg-viral-pipelineVIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
Python Apache License 2.0 UpdatedAug 23, 2024 -
VirID Public
Forked from ZiyueYang01/VirIDVirID: An integrated platform for the discovery and characterization of RNA Viruses
Python MIT License UpdatedJul 11, 2024 -
sim3C Public
Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
-
qc3C Public
Reference-free quality assessment for Hi-C sequencing data
-
CAT Public
Forked from MGXlab/CAT_packCAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Python MIT License UpdatedSep 12, 2023 -
ViralCC Public
Forked from dyxstat/ViralCCViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes
Python GNU General Public License v3.0 UpdatedJun 20, 2023 -
TMbed Public
Forked from BernhoferM/TMbedTransmembrane proteins predicted through Language Model embeddings
Python Apache License 2.0 UpdatedApr 6, 2023 -
nucleotide-transformer Public
Forked from instadeepai/nucleotide-transformer🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Python Other UpdatedApr 3, 2023 -
maw Public
Forked from solonas13/mawMAW: a suite on the computation and application of Minimal Absent Words
C++ GNU General Public License v3.0 UpdatedFeb 20, 2023 -
Nullomers-Assessor Public
Forked from gkoulouras/Nullomers-AssessorNullomers Assessor: A computational method for statistical evaluation of nullomers & minimal absent words
Python UpdatedFeb 20, 2023 -
bcubed Public
bcubed and weighted bcubed external validation index
Python GNU Affero General Public License v3.0 UpdatedJul 20, 2022 -
meta-sweeper Public
Parametric sweep of simulated microbial communities and metagenomic sequencing.
-
PlasClass Public
Forked from Shamir-Lab/PlasClassA tool to classify sequences of plasmid or chromosomal origin. A paper describing this tool is available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007781
Python MIT License UpdatedOct 29, 2021 -
genomics_notes Public
Forked from igordot/genomicsA collection of scripts and notes related to genomics and bioinformatics
R UpdatedOct 7, 2021 -
vHULK Public
Forked from LaboratorioBioinformatica/vHULKviral Host UnveiLing Kit (vHULK)
Python GNU General Public License v3.0 UpdatedAug 26, 2021 -
pygraphistry Public
Forked from graphistry/pygraphistryPyGraphistry is a Python library to quickly load, shape, embed, and explore big graphs with the GPU-accelerated Graphistry visual graph analyzer
Python BSD 3-Clause "New" or "Revised" License UpdatedAug 16, 2021 -
DeepVirFinder Public
Forked from papanikos/DeepVirFinderIdentifying viruses from metagenomic data by deep learning
-
GraphPlas Public
Forked from anuradhawick/GraphPlasGraphPlas: Assembly Graph Assisted Recovery of Plasmidic Contigs from TGS Assemblies
Python MIT License UpdatedJun 11, 2021 -
DRAM Public
Forked from WrightonLabCSU/DRAMDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Python GNU General Public License v3.0 UpdatedMay 19, 2021 -
i3seqdb Public
Tracking and workflow instrumentation for NGS
-
HiCzin Public
Forked from dyxstat/HiCzinHiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression
R MIT License UpdatedMar 20, 2021 -
GraphBin2 Public
Forked from metagentools/GraphBin2GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
Python GNU General Public License v2.0 UpdatedNov 23, 2020 -
Outbreak_EnrichmentCulture Public
Forked from chewbeckie/Outbreak_EnrichmentCultureNextflow UpdatedOct 28, 2020 -
{{ message }}