Find open-source science resources

List of resources on alternative splicing including software, databases, and other tools.

A port of [pyVCF](https://github.com/jamescasbon/PyVCF) using Cython for speed.

DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.

Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.

Natural Product-likeness calculator v-2.1 : calculates natural product-likeness of small molecules based on open-data of natural products.

GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.

GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.

Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.

A calculator incorporating various empirical pair and many-body potentials.

This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.

Tool to generate a count matrix for expression data in Galaxy. generate_count_matrix reads in one or more input text files with expression counts and produces a single combined file. Each input will have a column in the matrix containing expression values. The column containing gene (or feature) names should be identical for all input count files.

This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.

isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.

Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.

Statistical analysis of peptide microarrays

Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng).

DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders

Horizon chart D3-based JavaScript library for DNA data.

It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]

LogiCO contains the core concepts and properties used in the logistics domain, and mappings (as annotations) to UN/EDIFACTS Data elements.

An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.

CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.

This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor.

Recurrent breakpoint gene detection on copy number aberration profiles.

This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.

rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

This package provides a web interface to compute transcriptional regulatory modules with rTRM.

D3 JavaScript based genome viewer. Constructs SVGs.

The Annotation Ontology specification is currently used as input for the activities of the http://www.w3.org/community/openannotation/'>W3C Open Annotation Community Group that works towards a common, RDF-based, specification for annotating digital resources. The Group effort starts by working towards a reconciliation of two proposals that have emerged over the past two years: the http://code.google.com/p/annotation-ontology/'>Annotation Ontology and the http://www.openannotation.org/spec/beta/'>Open Annotation Model. Initially, editors of these proposals will closely collaborate to devise a common draft specification that addresses requirements and use cases that were identified in the course of their respective efforts. The goal is to make this draft available for public feedback and experimentation in the second quarter of 2012. The final deliverable of the Open Annotation Community Group will be a specification, published under an appropriate open license, that is informed by the existing proposals, the common draft specification, and the community feedback. [from homepage]

Automate common SAM & BAM conversions.

With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [Fellowship for Interpretation of Genomes (FIG)](http://thefig.info/) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. This prefix provides identifiers for molecular roles that describe the function of one or more proteins in microbes and plants.

Molecular property prediction with unified API for diverse models and respresentations,

Deep learning system for de novo design of high-affinity protein binders, achieving strong binding across diverse target classes including challenging intracellular proteins with significantly higher success rates than traditional wet-lab screening methods (Google DeepMind, Nature 2024)

Multimodal generative AI assistant for computational pathology enabling interactive visual-language conversations over histopathology images for diagnostic reasoning, case discussion, and education, built on a Mistral-7B backbone with domain-specific fine-tuning (Mahmood Lab, Harvard Medical School, 1.2K+ stars)

Google DeepMind and Google Quantum AI's transformer-based neural-network decoder for quantum error correction, trained on real Sycamore quantum processor data to outperform tensor-network and correlated matching decoders at code distances 3 and 5, demonstrating ML's role in enabling fault-tolerant quantum computing (Nature 2024)

Ecological modeling and conservation AI

Mathematical reasoning

A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations.

The R package dmGsea provides efficient gene set enrichment analysis specifically for DNA methylation data. It addresses key biases, including probe dependency and varying probe numbers per gene. The package supports Illumina 450K, EPIC, and mouse methylation arrays. Users can also apply it to other omics data by supplying custom probe-to-gene mapping annotations. dmGsea is flexible, fast, and well-suited for large-scale epigenomic studies.

Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data.

This software is meant to be used for classification of images of cell-based assays for neuronal surface autoantibody detection or similar techniques. It takes imaging files as input and creates a composite score from these, that for example can be used to classify samples as negative or positive for a certain antibody-specificity. The reason for its name is that I during its creation have thought about the individual picture as an archielago where we with different filters control the water level as well as ground characteristica, thereby finding islands of interest.

Provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.