https://github.com/choderalab/openmmtools • Rank 13.1 • Science 59%

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

brainstorm3 • Rank 10.1 • Science 62%

Brainstorm software: MEG, EEG, fNIRS, ECoG, sEEG and electrophysiology

obscure_stats • Rank 5.1 • Science 67%

A small collection of lesser-known statistical measures

hgtseq • Rank 5.1 • Science 67%

A pipeline to investigate horizontal gene transfer from NGS data

gnverifier • Rank 5.1 • Science 67%

GNverifier verifies scientific names against more than 100 biodiversity databases

deep-koalarization • Rank 8.1 • Science 64%

Keras/Tensorflow implementation of our paper Grayscale Image Colorization using deep CNN and Inception-ResNet-v2 (https://arxiv.org/abs/1712.03400)

ForestTools • Rank 13.1 • Science 59%

Detect and segment individual tree from remotely sensed data

CM++ - A Meta-method for Well-Connected Community Detection — Peer-reviewed • Rank 5.1 • Science 67%

CM++ - A Meta-method for Well-Connected Community Detection - Published in JOSS (2024)

regcm • Rank 8.1 • Science 64%

ICTP Regional Climate Model

callingcardstools • Rank 5.1 • Science 67%

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

pdb-tools • Rank 18.1 • Science 54%

A dependency-free cross-platform swiss army knife for PDB files.

ndn-python-repo • Rank 10.1 • Science 62%

An NDN Repo implementation in Python

com.github.ie3-institute:PowerSystemDataModel • Rank 10.1 • Science 62%

Provides an elaborated data model to model energy systems with a high granularity e.g. for bottom-up simulations. Additionally, useful functionalities to handle the model i/o are provided as well.

sars-cov-2-infektionen_in_deutschland • Rank 5.1 • Science 67%

Der vorliegende Datansatz enthält umfassende Informationen zu SARS-CoV-2-Infektionen in Deutschland, die gemäß dem Infektionsschutzgesetze (IfSG) von den Gesundheitsämtern an das Robert Koch-Institut (RKI) gemeldet wurden. Die Daten umfassen Informationen zur Anzahl der bestätigten Fälle, Todesfälle und Genesungen, aus denen sich weitere Kennzah...

https://github.com/cda-tum/mtct • Rank 5.1 • Science 67%

Design Automation for Railway Systems

yaeos • Rank 10.1 • Science 62%

Thermodynamic Equations of State, Fortran library with both automatic and anallytical derivation capabilities

solarstations • Rank 5.1 • Science 67%

A global catalog of solar irradiance monitoring stations.

aiida-kkr • Rank 13.1 • Science 59%

AiiDA plugin of the high-performance density functional theory code JuKKR (www.judft.de) for high-throughput electronic structure calculations.

forneylab.jl • Rank 8.1 • Science 64%

Julia package for automatically generating Bayesian inference algorithms through message passing on Forney-style factor graphs.

pytools • Rank 8.1 • Science 64%

iadpython • Rank 8.1 • Science 64%

Forward and Inverse radiative transfer models using the adding-doubling method in python.

freesurferformats • Rank 15.1 • Science 57%

GNU R package for reading and writing neuroimaging file formats. Not limited to FreeSurfer anymore, despite its name.

gemgis-data • Rank 5.1 • Science 67%

This repository contains the data used in GemGIS

bidsmreye • Rank 5.1 • Science 67%

BIDS app using deepMReye to decode eye motion for fMRI time series data.

deterministicparticleflowcontrol • Rank 5.1 • Science 67%

Repository for Deterministic Particle Flow Control framework

pydl • Rank 13.1 • Science 59%

Library of IDL astronomy routines converted to Python.

pyconcepticon • Rank 13.1 • Science 59%

Programmatic access to Concepticon data.

ml4floods • Rank 13.1 • Science 59%

An ecosystem of data, models and code pipelines to tackle flooding with ML🌊

NLSProblems • Rank 5.0 • Science 67%

Nonlinear Least Squares problems

agnpy • Rank 13.0 • Science 59%

Modelling jetted Active Galactic Nuclei radiative processes with python

https://github.com/libxsmm/libxsmm • Rank 13.0 • Science 59%

Library for specialized dense and sparse matrix operations, and deep learning primitives.

dromics • Rank 13.0 • Science 59%

Dose Response for Omics

genomeassembler • Rank 5.0 • Science 67%

Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads

hydroshoot • Rank 5.0 • Science 67%

Hydroshoot model for 3D hydraulic architecture simulation

pythia-foundations • Rank 8.0 • Science 64%

Jupyterbook source for the Foundations collection

lfpykernels • Rank 5.0 • Science 67%

Forward-model based calculations of causal spike-signal impulse response functions for finite-sized neuronal network models

ete3 • Rank 23.0 • Science 49%

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

https://github.com/sylabs/singularity • Rank 23.0 • Science 49%

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.

trove-newspaper-harvester • Rank 5.0 • Science 67%

cifplayer • Rank 5.0 • Science 67%

Minimalistic and fast HTML5 visualization of chemical structures in CIF, POSCAR, and OPTIMADE formats

https://github.com/atmoschem/vein • Rank 13.0 • Science 59%

R+Fortran+OpenMP package to estimate Vehicular Emissions INventories VEIN.

work-set-clustering • Rank 5.0 • Science 67%

A Python script to perform a clustering based on descriptive keys.

StochasticGroundMotionSimulation • Rank 5.0 • Science 67%

Ground-motion simulation via the Stochastic Method

atomate2 • Rank 23.0 • Science 49%

atomate2 is a library of computational materials science workflows

sperrorest • Rank 15.0 • Science 57%

Spatial error estimation and variable importance

tidyBdE • Rank 15.0 • Science 57%

R package that helps to retrieve data from Banco de España

RPANDA • Rank 13.0 • Science 59%

Phylogenetic ANalyses of DiversificAtion

geoh2 • Rank 5.0 • Science 67%

Geospatial analysis of green hydrogen production costs.

tennet • Rank 5.0 • Science 67%

Tensor network package

pyfaidx • Rank 23.0 • Science 49%

Efficient pythonic random access to fasta subsequences

knowledge-graph-language • Rank 5.0 • Science 67%

A query language for exploring knowledge graphs.

airavata • Rank 18.0 • Science 54%

A general purpose Distributed Systems Framework

biorecap • Rank 5.0 • Science 67%

Retrieve and summarize bioRxiv preprints with a local LLM using ollama

tomotwin-cryoet • Rank 10.0 • Science 62%

cryo-ET particle picking by representation and metric learning

speibase • Rank 4.9 • Science 67%

R code used in generating the SPEI global database.

rnssp • Rank 4.9 • Science 67%

A Signature R package for the National Syndromic Surveillance Program (NSSP) at the Centers for Disease Control and Prevention (CDC). A collection of tools, classes and functions that supports the Community of Practice of the NSSP.

hicar • Rank 4.9 • Science 67%

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

mlm-bias • Rank 4.9 • Science 67%

Measuring Biases in Masked Language Models for PyTorch Transformers. Support for multiple social biases and evaluation measures.

dft_pib_code • Rank 4.9 • Science 67%

Interactive Jupyter Notebooks for learning the fundamentals of Density-Functional Theory (DFT)

osemosys_pulp • Rank 4.9 • Science 67%

OSeMOSYS_PuLP: A Stochastic Modelling Framework for Long-Term Energy Systems Modeling

dragonflye • Rank 4.9 • Science 67%

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

constituent-treelib • Rank 4.9 • Science 67%

A lightweight Python library for constructing, processing, and visualizing constituent trees.

optimade.science • Rank 4.9 • Science 67%

A "sky-scanner" Optimade browser-only GUI

isnoda • Rank 4.9 • Science 67%

HRRR-ISNOBAL model setup using a conda environment and utilities to compare its output.

nanostringr • Rank 12.9 • Science 59%

NanoString QC, normalization, batch effect correction

vofotensors • Rank 4.9 • Science 67%

Bauer, J. K., & Böhlke, T. (2022). Variety of fiber orientation tensors. Mathematics and Mechanics of Solids, 10812865211057602.

rse • Rank 7.9 • Science 64%

tools for assessment and categorization of research software

distfit • Rank 17.9 • Science 54%

distfit is a python library for probability density fitting.

labelme • Rank 17.9 • Science 54%

Image Polygonal Annotation with Python (polygon, rectangle, circle, line, point and image-level flag annotation).

pronunciation-dictionary-utils • Rank 4.9 • Science 67%

Utils to modify pronunciation dictionaries.

scikit-datasets • Rank 4.9 • Science 67%

Scikit-learn-compatible datasets

argoonlineschool • Rank 4.9 • Science 67%

Here you can find find the source code of the Argo Online school.

minsh • Rank 4.9 • Science 67%

A minimal Python re-implementation of the A* with seed heuristic for exact global alignment (edit distance) in near-linear time

pykda • Rank 4.9 • Science 67%

Python package for the Kemeny Decomposition Algorithm (KDA) together with some Markov chain tooling.

text2vec • Rank 17.9 • Science 54%

text2vec, text to vector. 文本向量表征工具，把文本转化为向量矩阵，实现了Word2Vec、RankBM25、Sentence-BERT、CoSENT等文本表征、文本相似度计算模型，开箱即用。

concordexR • Rank 12.9 • Science 59%

Compute the neighborhood consolidation matrix and identify SHRs

rnpn • Rank 17.9 • Science 54%

R client for the National Phenology Network database API

bioreactor • Rank 4.9 • Science 67%

compression_benchmark • Rank 4.8 • Science 67%

Benchmarking FASTQ compression with 'mature' compression algorithms

ffdb • Rank 4.8 • Science 67%

nosql flat-file database and document storage

topformer • Rank 7.8 • Science 64%

TopFormer: Token Pyramid Transformer for Mobile Semantic Segmentation, CVPR2022

yolov7-sahi • Rank 4.8 • Science 67%

A lightweight vision library for performing large scale object detection & instance segmentation

packetmill • Rank 4.8 • Science 67%

PacketMill: Toward per-core 100-Gbps Networking

mmdetection3d-note • Rank 7.8 • Science 64%

mmdetection3d 代码重点注解笔记

pulsar-app • Rank 17.8 • Science 54%

Distributed job execution application built for Galaxy

atiim • Rank 4.8 • Science 67%

atiim: The Area Time Inundation Index Model

kgml_waterbody-area • Rank 4.8 • Science 67%

Using knowledge-guided machine learning to assess patterns of areal change in waterbodies across the contiguous US

TreeDist • Rank 12.8 • Science 59%

Calculate distances between phylogenetic trees in R

blockCV • Rank 12.8 • Science 59%

The blockCV package creates spatially or environmentally separated training and testing folds for cross-validation to provide a robust error estimation in spatially structured environments. See

ieeg • Rank 9.8 • Science 62%

A repo of current preprocessing methods for the Cogan Lab

plnmodels • Rank 12.8 • Science 59%

A collection of Poisson lognormal models for multivariate count data analysis

magpie4 • Rank 4.8 • Science 67%

R package | MAgPIE outputs R package for MAgPIE version 4.x

geoschem-gcpy • Rank 12.7 • Science 59%

Python toolkit for GEOS-Chem. Contains basic plotting scripts, plus the suite of GEOS-Chem benchmarking utilities.

brms • Rank 22.7 • Science 49%

brms R package for Bayesian generalized multivariate non-linear multilevel models using Stan

swatpy • Rank 4.7 • Science 67%

a set of python modules to work with the Soil and Water Assessment Tool (SWAT), including model run, programmatic config edits, simulation readouts and callibration with the fantastic SPOTPY package

cocolessons • Rank 4.7 • Science 67%

Course material for the bilingual (Spanish, English) Code to Communicate program.

waveorder • Rank 12.7 • Science 59%

Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.

exoctk • Rank 12.7 • Science 59%

The Exoplanet Characterization Tool Kit

pilgram • Rank 17.7 • Science 54%

A python library for instagram filters

eq5d • Rank 12.7 • Science 59%