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Defines a S4 class that is based on SingleCellExperiment. In

Family of generative single-cell foundation models (TF-Metazoa, TF

protein language models via sparse autoencoders, enabling mechanistic understanding of PLM representations

Experiments with expanded ensembles to explore chemical space.

We present a statistical simulator, scDesign3, to generate realistic single

protein abundance compared to conventional aggregation methods. This algorithm employs

protein binding pocket, enabling scaffold hopping and linker design workflows

Universal 3D molecular pretraining framework with 209M conformations, scaling to

RNA foundation model trained on millions of RNA sequences for

proteins trained on thousands of GPUs and Google TPUs using

Diffusion-based molecular docking achieving SOTA blind docking performance, treating

protein sequence design in the context of small-molecule ligands

LLM for scientific research papers

LLM agents across scientific domains

Large-scale biomolecular instruction dataset for chemistry/biology LLMs (ICLR2024)

protein sequence design (inverse folding) from backbone structures, achieving 52.4% sequence

Resources on ChIP-seq data which include papers, methods, links

UNIX-style FASTA manipulation tools.

The 'funOmics' package ggregates or summarizes omics data into higher

tidyFlowCore bridges the gap between flow cytometry analysis using the

Predicts whether an amino acid substitution affects protein function.

proteins) for nucleotide or protein sequences. Pipeline that screens for presence

protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors

A curated list of molecular docking software, datasets, and other

Protein-protein interaction data is essential for omics data analysis

This package provides functionalities for downstream analysis, annotation and visualizaton

[@crazyhottommy](https://github.com/crazyhottommy)'s notes on various steps and considerations

An R package that tests for enrichment and depletion of

function of one or more proteins in microbes and plants.

protein expression data. DecontX is a novel Bayesian method to computationally

Protein domains is one of the most import annoation of proteins

protein across multiple datasets. ProteoMM provides functionality for normalization, missing

protein-DNA binding on individual sequenced DNA molecules. For example

proteins form a major fraction of the druggable proteome and can be used

protein, ii) isolate individual synaptonemal complexes and measure their physical

Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse

proteins in various cellular processes by leveraging preexisting gene expression

Protein-Lipid Interaction Database. A large-scale experimentally validated dataset

protein sequence and NCBI taxonomy IDs (or RefSeq assembly accessions

protein-RNA binding with Deep Learning | This repository contains all DeepCLIP

method for prediction of ligand binding sites from protein structure.

Protein-protein interaction data is essential for omics data analysis

protein design and ligand screening by managing incompatible software environments

protein sequences across the microbial tree of life using structural