Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc. (@Merck)
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Top repositories

1

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.
Python
136
star
2

deepbgc

BGC Detection and Classification Using Deep Learning
Jupyter Notebook
122
star
3

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.
Java
106
star
4

r2rtf

Easily Create Production-Ready Rich Text Format (RTF) Table and Figure
R
76
star
5

DeepNeuralNet-QSAR

Python
64
star
6

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.
Python
48
star
7

rdf2x

RDF2X converts big RDF datasets to the relational database model, CSV, JSON and ElasticSearch.
Java
47
star
8

Sapiens

Sapiens is a human antibody language model based on BERT.
Jupyter Notebook
44
star
9

pkglite

Compact Package Representations
R
30
star
10

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.
Java
23
star
11

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.
Python
23
star
12

gsDesign2

Group Sequential Design Under Non-Proportional Hazards
R
19
star
13

AlgebraicAgents.jl

A lightweight framework to enable hierarchical, heterogeneous dynamical systems co-integration. Batteries included!
Julia
17
star
14

simtrial

Clinical trial simulation for time-to-event endpoints
R
17
star
15

metalite.ae

An R package for standard adverse events analysis
R
17
star
16

BioPhi-2021-publication

This repository contains scripts, data and jupyter notebooks used to produce the evaluation results in the BioPhi 2021 publication
Jupyter Notebook
15
star
17

metalite

An R package to create metadata structure for ADaM data analysis and reporting
R
15
star
18

PepSeA

Python
14
star
19

Mutation_Maker

Application for mutagenic primer design. Facilitates development of biocatalysts (Green Chemistry) and new therapeutic proteins.
Python
14
star
20

ReactiveDynamics.jl

A Julia package that implements a category of reaction (transportation) network-type dynamical systems.
Julia
14
star
21

boxly

Interactive box plot for clinical trial analysis
R
13
star
22

mRNAid

Jupyter Notebook
11
star
23

forestly

Interactive forest plot for adverse events analysis
R
11
star
24

pmpo

Probabilistic Multi-Parameter Optimization (pMPO)
Python
11
star
25

bgc-pipeline

Jupyter Notebook
9
star
26

AbLEF

Antibody Langauge Ensemble Fusion - fuses antibody structural ensemble and language representation for property prediction
Python
8
star
27

gMCPLite

Lightweight graph-based multiple comparison procedures
R
8
star
28

GeneratedExpressions.jl

A Julia package that implements a metalanguage to support expression comprehensions.
Julia
8
star
29

Data-Profiler

Java
8
star
30

gMCPShiny

A Shiny app for graphical multiplicity control
R
7
star
31

NNGP

Nearest Neighbor Gaussian Process
7
star
32

CEEDesigns.jl

A decision-making framework for the cost-efficient design of experiments, balancing the value of acquired experimental evidence and incurred costs.
Julia
7
star
33

rtdpy

Residence Time Distribution modeling in Python.
Python
6
star
34

matcher-mmpdb

Python
5
star
35

MolPROP

fuses molecular language and graph representation for property prediction
Python
5
star
36

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

Real-world Time to Treatment Discontinuation Prediction Algorithm
Perl
4
star
37

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.
Perl
4
star
38

TraceTrack

Python
3
star
39

gsdmvn

The goal of gsdmvn is to enable group sequential trial design for time-to-event endpoints under non-proportional hazards assumptions.
R
3
star
40

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
3
star
41

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.
TypeScript
3
star
42

helm-visualisation

JavaScript
2
star
43

OMOP-CONCEPT-EMBEDDING

Python
2
star
44

polo

POLO: web interface to MARCO-scored crystallization images
Python
2
star
45

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.
C++
2
star
46

BART-QSAR

R
1
star
47

3D_Tumor_Lightsheet_Analysis_Pipeline

Python
1
star
48

MicroMap_Pipeline

R
1
star
49

ProbeDesign

HTML
1
star
50

bayesiansprt

The goal of bayesiansprt (under GPL-3 license) is to provide the results for sequential probability ratio test under frequentist and Bayesian setup.
R
1
star
51

mmrm

R
1
star
52

rCPDMS

Chemoproteomics Data Analysis
R
1
star
53

Infant-Microbiome-Cohort

Infant Microbiome Cohort
Jupyter Notebook
1
star
54

psm3mkv

psm3mkv: A package to evaluate the fit and efficiency of three state oncology cost-effectiveness model structures
R
1
star