Sourcepredict 88% confidence

Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification - Published in JOSS (2019)

callingcardstools 84% confidence

A collection of objects and functions to work with calling cards sequencing tools. See docs at https://cmatkhan.github.io/callingCardsTools

pyrexMD 84% confidence

pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics - Published in JOSS (2021)

Opfi 84% confidence

Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets - Published in JOSS (2021)

SPyCi-PDB 84% confidence

SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. - Published in JOSS (2023)

Fireworks 84% confidence

Fireworks: Reproducible Machine Learning and Preprocessing with PyTorch - Published in JOSS (2019)

genbankpy 84% confidence

Tools to download, parse and filter GenBank files

mite_web 84% confidence

Repository for the MITE web presence

Fraggler 84% confidence

Fraggler: A Python Package and CLI Tool for Automated Fragment Analysis - Published in JOSS (2024)

KALMUS 84% confidence

KALMUS: tools for color analysis of films - Published in JOSS (2021)

elwaspatid 84% confidence

elwaspatid: A Python package to compute space-time diagrams for the propagation of elastic waves in 1D rods - Published in JOSS (2022)

GraphBin-Tk 69% confidence

GraphBin-Tk: assembly graph-based metagenomic binning toolkit - Published in JOSS (2025)

proteusPy 69% confidence

proteusPy: A Python Package for Protein Structure and Disulfide Bond Modeling and Analysis - Published in JOSS (2024)

SuchTree 63% confidence

SuchTree: Fast, thread-safe computations with phylogenetic trees - Published in JOSS (2018)

posebench 63% confidence

Comprehensive benchmarking of protein-ligand structure prediction methods. (ICML 2024 AI4Science)

TipToft 63% confidence

TipToft: detecting plasmids contained in uncorrected long read sequencing data - Published in JOSS (2019)

cerebra 63% confidence

cerebra: A tool for fast and accurate summarizing of variant calling format (VCF) files - Published in JOSS (2020)

OpenOmics 63% confidence

OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. - Published in JOSS (2021)

Corekaburra 63% confidence

Corekaburra: pan-genome post-processing using core gene synteny - Published in JOSS (2022)

SeqPanther 63% confidence

SeqPanther: Sequence manipulation and mutation statistics toolset - Published in JOSS (2023)

alignparse 63% confidence

alignparse: A Python package for parsing complex features from high-throughput long-read sequencing - Published in JOSS (2019)

ENASearch 63% confidence

ENASearch: A Python library for interacting with ENA's API - Published in JOSS (2017)

mutyper 63% confidence

mutyper: assigning and summarizing mutation types for analyzing germline mutation spectra - Published in JOSS (2023)

Python Implementation of Codon Adaptation Index 63% confidence

Python Implementation of Codon Adaptation Index - Published in JOSS (2018)

EUKulele 63% confidence

EUKulele: Taxonomic annotation of the unsung eukaryotic microbes - Published in JOSS (2021)

Badread 60% confidence

Badread: simulation of error-prone long reads - Published in JOSS (2019)

alpaca_eval 60% confidence

DPO evaluation

tabula 60% confidence

tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data - Published in JOSS (2019)

variation-normalization 60% confidence

Services and guidelines for normalizing variants

Mashtree 60% confidence

Mashtree: a rapid comparison of whole genome sequence files - Published in JOSS (2019)

Ngesh 41% confidence

Ngesh: a Python library for synthetic phylogenetic data - Published in JOSS (2021)

ReferenceSeeker 41% confidence

ReferenceSeeker: rapid determination of appropriate reference genomes - Published in JOSS (2020)

MemCNN 40% confidence

MemCNN: A Python/PyTorch package for creating memory-efficient invertible neural networks - Published in JOSS (2019)

eights 40% confidence

eights: BS 8888:2011 first angle projection drawings from FreeCAD 3D model - Published in JOSS (2019)

BAMnostic 40% confidence

BAMnostic: an OS-agnostic toolkit for genomic sequence analysis - Published in JOSS (2018)

MatchPy 40% confidence

MatchPy: Pattern Matching in Python - Published in JOSS (2018)

Finch 40% confidence

Finch: a tool adding dynamic abundance filtering to genomic MinHashing - Published in JOSS (2018)

Visualizing genome synteny with xmatchview 40% confidence

Visualizing genome synteny with xmatchview - Published in JOSS (2018)

grounded-segment-anything 40% confidence

nf-chai 40% confidence

POC Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction

ipal_evaluate 40% confidence

Intrusion Detection Evaluation - A framework to evalute (Industrial) Intrusion Detection Systems.

space-radiation-tolerant 40% confidence

Space Labs AI presents: A radiation-tolerant machine learning framework enabling neural networks to operate reliably in space environments. Features adaptive protection, Reed-Solomon error correction, and breakthrough architecture optimizations that improve performance under radiation.

random-array-kumaraswamy 40% confidence

Create an array containing pseudorandom numbers drawn from Kumaraswamy's double bounded distribution.

009-omnicontrol-control-any-joint-at-any-time-for-human-motion-generation 40% confidence

miassembler 40% confidence

Af-analysis 40% confidence

Af-analysis: a Python package for Alphafold analysis - Published in JOSS (2025)

ysoisochrone 40% confidence

ysoisochrone: A Python package to estimate masses and ages for YSOs - Published in JOSS (2025)

269-finalmlp-an-enhanced-two-stream-mlp-model-for-ctr-prediction 40% confidence

itrm 40% confidence

itrm: Interactive Terminal Utilities - Published in JOSS (2024)

RobotDART 40% confidence

RobotDART: a versatile robot simulator for robotics and machine learning researchers - Published in JOSS (2024)

A tool for qualitative data analysis designed to support computational thinking 40% confidence

A tool for qualitative data analysis designed to support computational thinking - Published in JOSS (2024)

SIRITVIS 40% confidence

SIRITVIS: Social Interaction Research Insights Topic Visualisation - Published in JOSS (2024)

HeuDiConv — flexible DICOM conversion into structured directory layouts 40% confidence

HeuDiConv — flexible DICOM conversion into structured directory layouts - Published in JOSS (2024)

PyRolL - An Extensible OpenSource Framework for Rolling Simulation 40% confidence

PyRolL - An Extensible OpenSource Framework for Rolling Simulation - Published in JOSS (2024)

Software Design and User Interface of ESPnet-SE++ 40% confidence

Software Design and User Interface of ESPnet-SE++: Speech Enhancement for Robust Speech Processing - Published in JOSS (2023)

GNS 40% confidence

GNS: A generalizable Graph Neural Network-based simulator for particulate and fluid modeling - Published in JOSS (2023)

A Java Library for Itemset Mining with Choco-solver 40% confidence

A Java Library for Itemset Mining with Choco-solver - Published in JOSS (2023)

oxDNA 40% confidence

oxDNA: coarse-grained simulations of nucleic acids made simple - Published in JOSS (2023)

VPsearch 40% confidence

VPsearch: fast exact sequence similarity search for genomic sequences - Published in JOSS (2022)

E2EDNA 2.0 40% confidence

E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands - Published in JOSS (2022)

Bam-readcount - rapid generation of basepair-resolution sequence metrics 40% confidence

Bam-readcount - rapid generation of basepair-resolution sequence metrics - Published in JOSS (2022)

TX$^2$ 40% confidence

TX$^2$: Transformer eXplainability and eXploration - Published in JOSS (2021)

Lerche 40% confidence

Lerche: Generating data file processors in Julia from EBNF grammars - Published in JOSS (2021)

Easy3D 40% confidence

Easy3D: a lightweight, easy-to-use, and efficient C++ library for processing and rendering 3D data - Published in JOSS (2021)

CutePeaks 40% confidence

CutePeaks: A modern viewer for Sanger trace file - Published in JOSS (2021)

microViz 40% confidence

microViz: an R package for microbiome data visualization and statistics - Published in JOSS (2021)

minimo 40% confidence

minimo: a linked data and metadata storage system for small labs - Published in JOSS (2021)

LibSWIFFT - A fast C/C++ Library for the SWIFFT Secure Homomorphic Hash Function 40% confidence

LibSWIFFT - A fast C/C++ Library for the SWIFFT Secure Homomorphic Hash Function - Published in JOSS (2021)

Off-resonance CorrecTion OPen soUrce Software (OCTOPUS) 40% confidence

Off-resonance CorrecTion OPen soUrce Software (OCTOPUS) - Published in JOSS (2021)

c-lasso - a Python package for constrained sparse and robust regression and classification 40% confidence

c-lasso - a Python package for constrained sparse and robust regression and classification - Published in JOSS (2021)

dantro 40% confidence

dantro: a Python package for handling, transforming, and visualizing hierarchically structured data - Published in JOSS (2020)

refsplitr 40% confidence

refsplitr: Author name disambiguation, author georeferencing, and mapping of coauthorship networks with Web of Science data - Published in JOSS (2020)

Graph Transliterator 40% confidence

Graph Transliterator: A graph-based transliteration tool - Published in JOSS (2019)

PDFIO 40% confidence

PDFIO: PDF Reader Library for native Julia - Published in JOSS (2019)

Spruceup 40% confidence

Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments - Published in JOSS (2019)

stardate 40% confidence

stardate: Combining dating methods for better stellar ages - Published in JOSS (2019)

math-iter-sequences-nonsquares 40% confidence

Create an iterator which generates a sequence of nonsquares.

tqsim 40% confidence

TQSim is an open-source anyon-based Topological Quantum Computing simulator

rnaseq-pipeline 40% confidence

Repository for the nf-core Hackathon demos

math-iter-sequences-positive-integers 40% confidence

Create an iterator which generates a positive integer sequence.

utils-async-function-sequence 40% confidence

Function sequence.

server 40% confidence

smolyax 40% confidence

smolyax: a high-performance implementation of the Smolyak interpolation operator in JAX - Published in JOSS (2025)

awesome-avd 40% confidence

A curated list of research resources in automated vulnerability detection (AVD)

roseui 40% confidence

Rose UI

iohub 40% confidence

Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata

slice-base-slice2seq 40% confidence

Convert a Slice object to a subsequence string.

prompt-engineer-for-revision-and-development 40% confidence

Guides, papers, lecture, notebooks and resources for prompt engineering

semibin2_dev 40% confidence

jetson-containers 40% confidence

Machine Learning Containers for NVIDIA Jetson and JetPack-L4T

bioregistry 40% confidence

📮 An integrative registry of biological databases, ontologies, and nomenclatures.

collapse 40% confidence

Advanced and Fast Data Transformation in R

lio-segmot 40% confidence

LiDAR-Inertial Odometry via Simultaneous Ego-motion Estimation and Multiple Object Tracking (ICRA 2023)

SaffronTree 39% confidence

SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs. - Published in JOSS (2017)

NCBImeta 37% confidence

NCBImeta: efficient and comprehensive metadata retrieval from NCBI databases - Published in JOSS (2020)

alv 34% confidence

alv: a console-based viewer for molecular sequence alignments - Published in JOSS (2018)

DendroPy 5 34% confidence

DendroPy 5: a mature Python library for phylogenetic computing - Published in JOSS (2024)

CAZy-parser a way to extract information from the Carbohydrate-Active enZYmes Database 34% confidence

CAZy-parser a way to extract information from the Carbohydrate-Active enZYmes Database - Published in JOSS (2016)

MetaGenePipe 34% confidence

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis - Published in JOSS (2023)

rainbow_bridge 30% confidence