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Pinned Repositories
BioPhi
BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.
deepbgc
BGC Detection and Classification Using Deep Learning
DeepNeuralNet-QSAR
Halyard
Halyard is an extremely horizontally scalable Triplestore with support for Named Graphs, designed for integration of extremely large Semantic Data Models, and for storage and SPARQL 1.1 querying of the whole Linked Data universe snapshots.
Line-of-Therapy-Algorithm
This is the Line of Therapy Algorithm, as described in the paper "Temporal phenotyping by mining healthcare data to derive lines of therapy for cancer" pending submission in the Journal of Biomedical Informatics.
matcher
Matcher is a tool for understanding how chemical structure optimization problems have been solved. Matcher enables deep control over searching structure/activity relationships (SAR) derived from large datasets, and takes the form of an accessible web application with simple deployment. Matcher is built around the mmpdb platform.
pkglite
Compact Package Representations
r2rtf
Easily Create Production-Ready Rich Text Format (RTF) Table and Figure
rdf2x
RDF2X converts big RDF datasets to the relational database model, CSV, JSON and ElasticSearch.
Sapiens
Sapiens is a human antibody language model based on BERT.
Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc.'s Repositories
Merck/deepbgc
BGC Detection and Classification Using Deep Learning
Merck/Halyard
Halyard is an extremely horizontally scalable Triplestore with support for Named Graphs, designed for integration of extremely large Semantic Data Models, and for storage and SPARQL 1.1 querying of the whole Linked Data universe snapshots.
Merck/Sapiens
Sapiens is a human antibody language model based on BERT.
Merck/BioPhi-2021-publication
This repository contains scripts, data and jupyter notebooks used to produce the evaluation results in the BioPhi 2021 publication
Merck/Data-Profiler
Merck/gMCPShiny
A Shiny app for graphical multiplicity control
Merck/matcher-mmpdb
Merck/compoundcomplexity
This is an implementation of Compound Complexity for use in the SMART-PMI as described by Sherer et al. It contains derived training data as required by the described Random Forest Model in order to replicate data presented in paper as well as applying to novel data.
Merck/gsdmvn
The goal of gsdmvn is to enable group sequential trial design for time-to-event endpoints under non-proportional hazards assumptions.
Merck/polo
POLO: web interface to MARCO-scored crystallization images
Merck/Real-world-Time-to-Treatment-Discontinuation-Prediction-Algorithm
Real-world Time to Treatment Discontinuation Prediction Algorithm
Merck/TraceTrack
Merck/deker
This library is made to perform feature selection based on a method originally proposed in by Sun et al. [1]. This library specifically relates to the methodology described in [2], named DEKER for decomposed kernel regression, which includes methods for identifying optimal hyperparameter values. This library was also designed for use in the context of network inference, also described in [2], by iteratively reapplying the DEKER method for feature selection across all features of a dataset.
Merck/helm-visualisation
Merck/OMOP-CONCEPT-EMBEDDING
Merck/3D_Tumor_Lightsheet_Analysis_Pipeline
Merck/bayesiansprt
The goal of bayesiansprt (under GPL-3 license) is to provide the results for sequential probability ratio test under frequentist and Bayesian setup.
Merck/Infant-Microbiome-Cohort
Infant Microbiome Cohort
Merck/MicroMap_Pipeline
Merck/mmrm-openpharma
Mixed Models for Repeated Measures (MMRM) in R.
Merck/skorch
A scikit-learn compatible neural network library that wraps PyTorch
Merck/bards-aactreveal
Provides tools for extracting and querying data from the AACT (Aggregate Content of ClinicalTrials.gov) database for subsequent analyses.
Merck/ChemicalSpaceGeneration
Merck/DTedit
Editable DataTables for shiny apps
Merck/FPFN
Merck/GoNoGo
Merck/maicplus
Merck/NLP-SLR-corpora
The use of systematic literature reviews (SLR) is an important tool for life-science research. SLRs are manually intensive procedures involving selection and retrieval of relevant publications, typically by human review of their abstracts. The shared two disease-specific corpora were developed for this purpose. One is for human papillomavirus (HPV) associated diseases and the other is for pneumococcal-associated pediatric diseases (PAPD).
Merck/Parmsurv
a SAS marco on parametric survival analysis
Merck/Photoproximity_Labeling
This code is provided to replicate the analysis performed for the publication "Exploring Cellular Microenvironments via Photocatalytic Carbene Generation".