Recently Published Apps

1. CellTypist: Automated cell type annotation in single-cell RNA-seq data. It uses pre-trained machine learning models on curated datasets to deliver fast, standardized, and reproducible cell labeling. This is especially valuable for large-scale immunology and tissue profiling studies, reducing manual effort and subjectivity. 
2. GATK VariantToTable: Transform raw VCF data into clean, structured tables. Select the INFO, FORMAT, or genotype fields you need, and the tool generates a ready-to-use CSV/TSV file for effortless filtering, visualization, and downstream analysis in Excel, R, and Python. 
3. GATK GenomicsDBImport: Efficiently combine multiple gVCF files into a GenomicsDB workspace, enabling scalable joint genotyping. It organizes variant data in a tiled database format, which allows faster queries and reduces storage requirements compared to raw gVCFs. This step is typically performed before running GenotypeGVCFs in large cohort analyses. The updated version 4.6.2.0, now featuring a DB update option.
4. The MCmicro workflow: A scalable and reproducible pipeline for processing multiplexed tissue imaging data. It integrates tools for image registration, illumination correction, segmentation, and feature extraction. These tools produce high-quality single-cell spatial datasets and are designed for large-scale studies, MCmicro standardizes analysis across experiments, enabling downstream biological insights from multiplex imaging platforms. This updated workflow version, with existing models and support for custom models.

Megha Roy