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NIM Studio is a local-first platform for neuroinformatics, BIDS organization, metadata generation, duplicate auditing, and scalable research data management.

A bioinformatics tool for viewing and calculating base modification frequencies from BAM files

Simple test framework for Nextflow pipelines

Reactr is an modularized, Snakemake workflow for automated, species-agnostic characterization of gene families from sequence to experimental design. Given a query protein sequence and NCBI taxonomy IDs (or RefSeq assembly accessions), reactr retrieves genomic data and runs comprehensive analysis across 4 integrated tiers: (1) evolutionary analysis, including homolog detection, domain-based clustering, multiple sequence alignment, and phylogenetic inference; (2) synteny and selection analysis, detecting collinear blocks and calculating Ka/Ks ratios; (3) structural and regulatory characterization, including motif discovery, chromosomal mapping, biochemical property prediction, subcellular localization prediction, and promoter analysis; and (4) experimental design tools, generating PCR primers and scored CRISPR gRNAs for lab validation. Reactr bridges computational prediction and experimental validation, thus enabling rapid transition from genomic discovery to functional studies.

Harmonize numerical values extracted from medical images (e.g. acquired with different models of image-acquisition system)

Browser-based viewer for GenBank and GenPept files. Renders an interactive linear and circular feature map, the annotated source text, and the nucleotide/protein sequence side by side. Translates CDS features using the record's own genetic code and translation qualifiers, flags where the stored /translation disagrees with a plain translation, and adds optional computed layers: ORF prediction and restriction-site mapping. Handles multi-record files. Runs entirely in the browser — files are never uploaded.

ArrayAnalysis is a web-based application for transcriptomic data analysis. It supports the analysis of both microarray and RNA-seq data. The tool may also be installed locally as a desktop app, Docker image, or R package.

Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source. A key feature of Supernova is that it creates diploid assemblies, thus separately representing maternal and paternal chromosomes over very long distances. Almost all other methods instead merge homologous chromosomes into single incorrect 'consensus' sequences. Supernova is the only practical method for creating diploid assemblies of large genomes.