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an open source deep learning platform that provides a seamless path from research prototyping to production deployment.

scGPT is a foundation model for Single-Cell Multi-omics using generative AI. scGPT can be optimized to achieve superior performance across diverse downstream applications such as cell type annotation, multi-batch integration, multi-omic integration, perturbation response prediction and gene network inference

rapid and standardized annotation of bacterial genomes & plasmids.

Copy-number Haplotype Inference in Single-cell by Evolutionary Links

CHISEL is an algorithm to infer allele- and haplotype-specific copy numbers in individual cells from low-coverage single-cell DNA sequencing data (e.g., those generated by Direct Library Preparation+ (DLP+), 10x Genomics CNV Solution, DOP-PCR, etc.).

a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy (GTDB).

a Python/Rust implementation for GSEA and wrapper for Enrichr. GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It can be used for convenient GO enrichment and to produce publication quality figures in python.

a reactive workflow framework and programming DSL that ease writing computational pipelines with complex data.

It is designed around the idea that the Linux platform is the lingua franca of data science. Linux provides many simple but powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations.

Nextflow extends this approach, adding the ability to define complex program interactions and a high-level parallel computational environment based on the dataflow programming model.

A Nextflow script is defined by composing many different processes. Each process can be written in any scripting language that can be executed by the Linux platform (BASH, Perl, Ruby, Python, etc), to which is added the ability to coordinate and synchronize the processes execution by simply specifying their inputs and outputs.

a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.

a flexible read trimming tool for Illumina NGS data.

a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.