Merck/mRNAid

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Created over 2 years ago
Updated 7 months ago

Merck/mRNAid

Merck

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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

Jupyter Notebook

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.

r2rtf

Easily Create Production-Ready Rich Text Format (RTF) Table and Figure

DeepNeuralNet-QSAR

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.

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.

Jupyter Notebook

pkglite

Compact Package Representations

sonar-r-plugin

Adds support for R language into SonarQube. It uses output from lintr tool which is processed by the plugin and uploaded into SonarQube server.

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.

gsDesign2

Group Sequential Design Under Non-Proportional Hazards

AlgebraicAgents.jl

A lightweight framework to enable hierarchical, heterogeneous dynamical systems co-integration. Batteries included!

simtrial

Clinical trial simulation for time-to-event endpoints

metalite.ae

An R package for standard adverse events analysis

BioPhi-2021-publication

This repository contains scripts, data and jupyter notebooks used to produce the evaluation results in the BioPhi 2021 publication

Jupyter Notebook

metalite

An R package to create metadata structure for ADaM data analysis and reporting

PepSeA

Mutation_Maker

Application for mutagenic primer design. Facilitates development of biocatalysts (Green Chemistry) and new therapeutic proteins.

ReactiveDynamics.jl

A Julia package that implements a category of reaction (transportation) network-type dynamical systems.

boxly

Interactive box plot for clinical trial analysis

forestly

Interactive forest plot for adverse events analysis

pmpo

Probabilistic Multi-Parameter Optimization (pMPO)

bgc-pipeline

Jupyter Notebook

AbLEF

Antibody Langauge Ensemble Fusion - fuses antibody structural ensemble and language representation for property prediction

gMCPLite

Lightweight graph-based multiple comparison procedures

GeneratedExpressions.jl

A Julia package that implements a metalanguage to support expression comprehensions.

Data-Profiler

gMCPShiny

A Shiny app for graphical multiplicity control

NNGP

Nearest Neighbor Gaussian Process

CEEDesigns.jl

A decision-making framework for the cost-efficient design of experiments, balancing the value of acquired experimental evidence and incurred costs.

rtdpy

Residence Time Distribution modeling in Python.

matcher-mmpdb

MolPROP

fuses molecular language and graph representation for property prediction

Real-world-Time-to-Treatment-Discontinuation-Prediction-Algorithm

Real-world Time to Treatment Discontinuation Prediction Algorithm

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.

TraceTrack

gsdmvn

The goal of gsdmvn is to enable group sequential trial design for time-to-event endpoints under non-proportional hazards assumptions.

curation-open-source

This wrapper enables the HPC execution of FDA DB curation and list all the step in a programming language style.

Jupyter Notebook

Message-Hub

The Messaging Orchestration HUB will be responsible for providing a connection between an organization's GS1 EPCIS-based track and trace data source system (for example ATTP) and the blockchain networks that require data relevant to product serialization and track & trace.

helm-visualisation

OMOP-CONCEPT-EMBEDDING

polo

POLO: web interface to MARCO-scored crystallization images

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.

BART-QSAR

3D_Tumor_Lightsheet_Analysis_Pipeline

MicroMap_Pipeline

ProbeDesign

bayesiansprt

The goal of bayesiansprt (under GPL-3 license) is to provide the results for sequential probability ratio test under frequentist and Bayesian setup.

mmrm

rCPDMS

Chemoproteomics Data Analysis

Infant-Microbiome-Cohort

Infant Microbiome Cohort

Jupyter Notebook

psm3mkv

psm3mkv: A package to evaluate the fit and efficiency of three state oncology cost-effectiveness model structures