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METEOR is a plateform for quantitative metagenomics profiling of complex

ViralQuest is an interactive pipeline designed for the post-assembly

plot protein-protein interaction networks, all from inside of R.

protein marker channels. simpleSeg can also be used for the normalization

Neural network-based cryo-EM heterogeneous reconstruction, modeling continuous 3D

protein-protein interaction screening with AlphaFold-Multimer and AlphaFold 3, supporting

This R package supports the handling and analysis of imaging

protein folding and interactions. It calculates polar interaction changes and analyzes

An ultrafast protein aligner for `blastp` and `blastx` like searches.

Visualisation of peptide isotopic peaks and SIP peptide spectra match

ViralClust is a modular Nextflow pipeline designed for bias-aware

netZooR unifies the implementations of several Network Zoo methods (netzoo

protein particles in micrographs at competitive precision with far fewer

Convert AMBER forcefields from ANTECHAMBER to GROMACS format.

protein structure search using a learned 3Di structural alphabet (VQ-VAE) that

kTYPr is an in silico tool designed to map the

protein-protein interaction (PPI) networks. GCN inference relies on the popular

Suite of tools to handle gene annotations in any GTF/GFF

BgeeCall allows to generate present/absent gene expression calls without using

COSMOS (Causal Oriented Search of Multi-Omic Space) is a

protein embeddings and bidirectional transformer architecture (Cantini Lab, 148+ stars

OxyMetaG is a tool that estimates the proportional abundance of

Protein Atlas data. HPAanalyze is designed to fullfill 3 main

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

protein-protein interaction (PPI) sites, designed to handle both structured

DupyliCate is a high-throughput Python tool designed for mining

A local command-line tool for ancestral sequence reconstruction with

protein isoforms. Our approach infers the presence/absence of protein isoforms

Collection of functions to calculate a nucleotide sequence surrounding for

protein stability of the transcription factors (TFs) of the TSGs

GraphExperiment provides users and developers with an S4 class that

Fit linear models to overdispersed count data. The package can

immune escape in proteins like SARS-CoV-2 S proteins.

`orthogene` is an R package for easy mapping of orthologous

Bayesian priors to increase power to detect differentially abundant proteins.

CPSM provides a comprehensive computational pipeline for predicting survival probability

protein-protein interactions), by including network-based regularizers. glmSparseNet uses

protein domain-based approach and; iii. synteny detection using synteny

A generic but comprehensive bacterial annotation pipeline, built with Nextflow

Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR

Prokka: rapid prokaryotic genome annotation. Prokka is one of the

protein motif analysis and visualization in R. PMScanR facilitates the identification

protein binding signals from ChIP-seq and sequence motif information

protein expression, pathway activity, etc.), based on the union occurence

proteins with potential clinical associations. From CNA and RNA-seq data

Protein coding genes from a list of candidates. Systematically download

protein sequences and classify them based on their modes of duplication

protein sequences and analyze them. Anchor pairs are detected with

Coralysis is an R package featuring a multi-level integration

protein markers at the single-cell level, producing high dimensional