Center for Computational Biomedicine

Harvard Medical School

United States of America

Pinned Repositories

BioPlex
R-side access to PPI data from Gygi lab
Language:R5 3 172
BioPlexAnalysis
Applications and downstream analysis of BioPlex PPI data
Language:R41
computervision
Everything to get started with computer vision
Language:Jupyter Notebook40
docker-analytic-workbench
Language:Dockerfile30
docker-rstudio-server
A repository for RStudio Server containers, with the goal of providing multi-architecture (ARM64 and AMD64) images.
Language:Dockerfile40
HarvardInovalonUserGuide
User guide for Harvard's Inovalon resources.
Language:R4 4 22
HuBMAPy
A package to query the HuBMAP Human Reference Atlas Ontology
Language:Python12
MerfishData
Collection of public MERFISH datasets
Language:R01
nhanes-database
Language:R3 5 1044
ontology-mapper
a tool for mapping free-text descriptions of entities to ontology terms
Language:Python13 4 233

Center for Computational Biomedicine's Repositories

ccb-hms/ontology-mapper
a tool for mapping free-text descriptions of entities to ontology terms
Language:Python13 4 233
ccb-hms/computervision
Everything to get started with computer vision
Language:Jupyter Notebook40
ccb-hms/HarvardInovalonUserGuide
User guide for Harvard's Inovalon resources.
Language:R4 4 22
ccb-hms/nhanes-database
Language:R3 5 1044
ccb-hms/phonto
PHenome - PHenome ONTOlogy for NHANES
Language:R3 9 311
ccb-hms/BioPlexPy
Python-side access to PPI data from Gygi lab
Language:Jupyter Notebook2 5 121
ccb-hms/gwasCatSearch
tooling for semantic search of NHGRI GWAS catalog
Language:R11
ccb-hms/NHANES-metadata
Language:Python11
ccb-hms/workbench-python-workshop
8-hour workshop introducing Python using The Carpentries new workbench template.
1 5 0
ccb-hms/GWASCatalogSearchDB
Language:Python00
ccb-hms/Imputation
Imputation methods for biomedical data
Language:HTML00
ccb-hms/ontology-mapper-ui
Language:JavaScript0 2 131
ccb-hms/AlphaMissenseR
Accessing AlphaMissense Data Resources in R
Language:R
ccb-hms/bioc-chat-bot-testing
Testing for Bioconductor chatbots
Language:Jupyter Notebook
ccb-hms/esm
Evolutionary Scale Modeling
Language:Jupyter Notebook
ccb-hms/faiss-cpu-docker-workbench
A dockerized Jupyter notebook for completing AI tasks with faiss, openai, and lang chain.
Language:Python
ccb-hms/getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
ccb-hms/MedEd-AI
Language:Jupyter Notebook
ccb-hms/MouseAgingData
Mouse aging multi-omics project with Rubin Lab
Language:R
ccb-hms/nhanes-data
Language:R
ccb-hms/nhanes-exploration
Exploring NHANES data through the nhanesA package
Language:HTML
ccb-hms/nhanes_stan
Language:R
ccb-hms/ollama-at-HMS
Documentation, scripts, tutorials, presentations, wikis, etc. that relate to running and interacting with text LLM models using `ollama` on HMS O2
ccb-hms/ollama-rag-workshop
Dockerized jupyter notebooks for doing retrieval-augmented generation with ccb's ollama instance. Part of the introductory ollama workshop.
Language:Jupyter Notebook
ccb-hms/ontology-mapper-evaluation
Resources to reproduce the comparison of ontology mappings generated by text2term and select benchmark mapping sets
Language:Python
ccb-hms/osca-workbench
Single-cell RNAseq materials derived from the 2023 ISMB OSCA workshop in the carpentries workbench format.
Language:R
ccb-hms/sbert-scispacy-tools
tools for NER with scispacy and sentence embeddings with sbert
Language:Python
ccb-hms/scDiagnostics
Diagnostic functions to assess the quality of cell type annotations in single-cell RNA-seq data
Language:R1
ccb-hms/stan_workshop_data
ccb-hms/text-detection
text detection from natural images using EAST algorithm
Language:Python