Scientific Open Source Software

The Pattern Institute maintains a curated listing of scientific open source software developed and supported by its research community. This collection includes R packages, data packages and reproducible compendia designed to advance computational biology, genomics, and data science. Each software entry is openly available, documented, and actively maintained to promote reproducibility, collaboration, and innovation in scientific research.

R Packages

A collection of R packages maintained by PI’s community.

quincunx

R

Human Genetics

Polygenic Risk Score

PGS Catalog

Programmatic access to the PGS Catalog. This package provides easy access to ‘PGS’ Catalog data by accessing the REST API.

sdtm.oak

R

CDISC

SDTM

clinical data

An EDC and Data Standard agnostic SDTM data transformation engine that automates the transformation of raw clinical data in ODM format to SDTM based on standard mapping algorithms.

ensemblr

R

Genetics

Ensembl

R client for the Ensembl REST API.

grantham

R

Grantham distance

missense mutations

evolution

The goal of grantham is to provide a minimal set of routines to calculate the Grantham distance (Grantham (1974)).

mgi.report.reader

R

Genetics

Mouse

Mouse Genome Informatics (MGI)

Gene Nomenclature

Provides readers for easy and consistent importing of Mouse Genome Informatics (MGI) report files.

gwasrapidd

R

Human Genetics

Genome-wide Association Study

GWAS Catalog

R package to query, download and wrangle GWAS Catalog data; provides easy access to the NHGRI-EBI GWAS Catalog data by accessing the REST API.

hgnc

R

HGNC

Human Genetics

Easily download and import the latest HGNC complete gene data set into R.

fluents

R

ODE

dynamical system

grind

Phase plane analysis of low-dimensional ordinary differential equation models.

glfw

R

C

GLFW

OpenGL

R Interface to the GLFW C Library.

agvgd

R

AGVGD

missense substitutions

Provides an R implementation of the Align-GVGD (A-GVGD) method.

Data Packages

A collection of data packages that help with ecological modelling.

CAOP.RAA.2024

R

data

Azores

Direção-Geral do Território

CAOP

Região Autónoma dos Açores

sf

spatial analysis

Provides the 2024 official administrative boundaries of the Azores (Região Autónoma dos Açores (RAA)) by Direção-Geral do Território (DGT).

azores.seamounts

R

data

Azores

seamount

atlantic ocean

Provides easy access in R to seamount details provided in Table A1 in Morato et al. (2008).

azores.bathymetry

R

data

Azores

bathymetry

atlantic ocean

Easily generate SpatRaster objects for bathymetry, depth, elevation and slope at sea in the Azores.

eunis.habitats

R

data

EUNIS

habitat

R data package that provides the EUNIS habitat classification in tidy format.

Compendium Packages

R packages supporting reproducibility for publications.

azores.fkw

R

compendium

Azores

false-killer whales

R compendium for Peres dos Santos et al. (2025).

PCR Data Packages

A collection of data packages to support the development and assessment of qPCR model fitting.

lievens

R

data

Real-Time qPCR

Lievens

Real-Time PCR Data Sets by Lievens et al. (2012).

vermeulen

R

data

Real-Time qPCR

Vermeulen

Real-Time PCR Data Sets by Vermeulen et al. (2009).

karlen

R

data

Real-Time qPCR

Karlen

Real-Time PCR Data Sets by Karlen et al. (2007).

sisti

R

data

Real-Time qPCR

Sisti

Real-Time PCR Data Sets by Sisti et al. (2010).

boggy

R

data

Real-Time qPCR

Boggy

Real-Time PCR Data Sets by Boggy et al. (2010).

batsch

R

data

Real-Time qPCR

Batsch

Real-Time PCR Data Sets by Batsch et al. (2008).

ruijter

R

data

Real-Time qPCR

Ruijter

Real-Time PCR Data Sets by Ruijter et al. (2013).

rutledge

R

data

Real-Time qPCR

Rutledge

Real-Time PCR Data Sets by Rutledge et al. (2004).

guescini

R

data

Real-Time qPCR

Guescini

Real-Time PCR Data Sets by Guescini et al. (2008).