https://github.com/lumol-org/lumol
Universal extensible molecular simulation engine
HiCcompare
Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices
volkszaehler.org
Open Source Smart Meter with focus on privacy - you remain the master of your data.
ccm
Apache Cassandra® Cluster Manager (CCM) – easily create and destroy clusters on localhost
gtfsrouter
Routing and analysis engine for GTFS (General Transit Feed Specification) data
https://github.com/bzrudski/antnuptracker-server
Server application for AntNupTracker for recording ant nuptial flights
https://github.com/annakrystalli/dataspice-tutorial
Tutorial in practical research data management: creating simple metadata files using dataspice
https://github.com/alan-turing-institute/rctab-infrastructure
Azure infrastructure as code for RCTab
https://github.com/aclai-lab/solereasoners.jl
This package provides algorithms for reasoning, namely including a sat solver and an automatic theorem prover both based on analytic tableau technique.
https://github.com/acdh-oeaw/tei-abstracts-app
Web App to publish the Abstracts of TEI-2016
https://github.com/bionanoimaging/psftoolbox-matlab
Includes various ways to calculate point spread functions (PSFs) with a focus on high NA fluorescence microscopy.
https://github.com/broadinstitute/backstage
Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
https://github.com/bertsky/docstruct
Document structure detection from PAGE-XML to METS-XML
https://github.com/cbg-ethz/jnotype
Probabilistic modeling of high-dimensional binary data in JAX
https://github.com/aise-tudelft/stacc
STACC: a set of SentenceTransformer Assisted Comment Classifiers
https://github.com/amlalejini/signalgp
New implementation of SignalGP virtual hardware.
https://github.com/astrazeneca/selfpad
The official implementation of "Improving Antibody Humanness Prediction using Patent Data".
https://github.com/astropy/repo_stats
Git and citation stats for your repo and papers
https://github.com/broadinstitute/gatk-tool-wdls
Autogenerated WDLs for GATK Tools
https://github.com/biocypher/omnipath-secondary-adapter
BioCypher adapter to retrieve data from Omnipath database (Networks, Intercell, Complexes, EnzymePTM and Annotations).
https://github.com/cole-monnahan-noaa/mixed_resids
Residual analysis for spatial models
https://github.com/alleninstitute/neuropixels_platform_paper
Code used to generate figures for Siegle, Jia et al. (2019)
https://github.com/datos-fundar/complejidad_economica_verde
Desarrollo de cálculos varios de complejidad económica
https://github.com/chaoss/grimoirelab-kidash
Kidash: A GrimoireLab tool & library to manage Kibana/Kibiter visualizations and dashboards
dataquieR 2
dataquieR 2: An updated R package for FAIR data quality assessments in observational studies and electronic health record data - Published in JOSS (2024)
htmltab
❗ Fork of the abandoned https://github.com/crubba/htmltab with the aim to keep it on CRAN. Expect minimal support.
digittests
digitTests is an R package providing statistical tests for detecting irregular digit patterns. The package is also implemented with a graphical user interface in the Audit module of JASP (www.jasp-stats.org), a free and open-source statistical software program.
LambertW
LambertW R package: Lambert W x F distributions and Gaussianization for skewed & heavy-tailed data
t81_558_deep_learning
T81-558: Keras - Applications of Deep Neural Networks @Washington University in St. Louis
DTSg
A Class for Working with Time Series Data Based on 'data.table' and 'R6' with Largely Optional Reference Semantics (Development Version)
https://github.com/cornelllabofornithology/ebird-best-practices
Best Practices for Using eBird Data
pyorc
Surface velocity, object tracking, and river flow measurements in an open-source API
cosore
Data, metadata, and software tools for the COSORE database of continuous soil respiration measurements
https://github.com/cancervariants/disease-normalization
Services and guidelines for normalizing disease terms
py-smote-variants
A collection of 85 minority oversampling techniques (SMOTE) for imbalanced learning with multi-class oversampling and model selection features
https://github.com/metrics-js/process
Module for collecting different process and system metrics and providing them as a metric stream
traitdataform
A package to manage and compile functional trait data into predefined templates
https://github.com/deepskies/deepsurveysim
An astrological survey simulation designed for testing MDP-style algorithms
https://github.com/alejandrogzi/bed2gff
cool BED-to-GFF3 converter that runs in parallel
https://github.com/datejada/generation-expansion-planning-models
Generation Expansion Planning (GEP) models considering uncertainties on renewable energy resources (RES)
https://github.com/alleninstitute/coupledae-patchseq
Multimodal data alignment and cell type analysis with coupled autoencoders.
https://github.com/bonsai-rx/python-scripting
Bonsai Scripting Library for interfacing with the Python runtime
https://github.com/bytedance/deer-flow
DeerFlow is a community-driven Deep Research framework, combining language models with tools like web search, crawling, and Python execution, while contributing back to the open-source community.
https://github.com/static-frame/frame-fixtures
Use compact expressions to create diverse, deterministic DataFrame fixtures with StaticFrame
https://github.com/biigle/geo
:m: BIIGLE module to explore images on a world map
https://github.com/crowdstrike/remark-preset-lint-crowdstrike
remark-lint preset for CrowdStrike
https://github.com/spiceai/spiceai
A portable accelerated SQL query, search, and LLM-inference engine, written in Rust, for data-grounded AI apps and agents.
spacy-wrap
spaCy-wrap is a wrapper library for spaCy for including fine-tuned transformers from Huggingface in your spaCy pipeline allowing you to include existing fine-tuned models within your SpaCy workflow.
phsmethods
An R package to standardise methods used in Public Health Scotland (https://public-health-scotland.github.io/phsmethods/)
https://github.com/nixtla/statsforecast
Lightning ⚡️ fast forecasting with statistical and econometric models.
https://github.com/cqcl/pytket-qulacs
pytket-qulacs, extensions for pytket quantum SDK
bristlecone
An F# library for mechanistic modelling of ecological time series data
https://github.com/erictleung/shinydiversity
Interactive application to explore various ecological diversity metrics
RRPP
RRPP: An R package for fitting linear models to high-dimensional data using residual randomization
https://github.com/caltechlibrary/rdmworkbook
bookdown files for "The Research Data Management Workbook"
https://github.com/caltechlibrary/dibsiiif
Scripts to support the Caltech Library DIBS application
https://github.com/broadinstitute/viral-references
Reference tables for viral genomics
https://github.com/chiang-yuan/prodar
PyTorch implementation of Protein Dynamically Activated Residues (ProDAR) for dyamics-informed protein function prediction/annotation
https://github.com/cmadan/mridataviz
Supplementary to "Data visualization for inference in tomographic brain imaging"
https://github.com/broadinstitute/terra-featured-workspace-tests
This code is to test that terra featured workspaces are working properly