Find open-source science resources

RAiSD-AI is a tool for training, testing, and deploying Convolutional Neural Networks to detect selective sweeps in genomic data, extending the functionality of the original RAiSD software with machine learning capabilities. It supports SNP data processing, CNN model training with TensorFlow or PyTorch, and genome-wide selective sweep detection.

Exact, validated excision of coordinate-defined genomic regions from transposed NEXUS matrices.

dadi is a bioinformatics tool for inferring demographic history and selection from genetic data using diffusion approximations, offering speed and flexibility in modeling population dynamics. It supports up to three populations with customizable parameters and provides efficient computational performance.

A Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.

GAIn is a platform for annotating genetic variants, genomic positions, and regions with reproducible, declarative pipelines using curated Genomic Resource Repositories.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

NuclearPhaser is a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs. This is an overview of the phasing pipeline for dikaryons.

Pan.bio is a cloud genomics platform for pipeline execution, exploratory analysis, and clinical variant interpretation. Workflows runs validated Nextflow and nf-core pipelines including Sarek, rnaseq, scrnaseq, mag, ampliseq, chipseq and atacseq without local installation. Notebooks provides Python and R sessions with a preinstalled bioinformatics stack, importing public data from GEO, SRA and IPG by accession and reading Workflows outputs directly. VAIC applies ACMG/AMP variant classification with gene-specific rule sets from CanVIG-UK and ClinGen ENIGMA, with automated evidence criteria implemented for BRCA1 and BRCA2. Cohorts provides federated analysis of patient data within a Trusted Research Environment.