Pinned Repositories
af2complex
Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
alphamap
An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
AMBERff-in-NAMD
AMRFinderPlus
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
are_you_still_using_elbow_method
autogluon
AutoGluon: AutoML for Text, Image, and Tabular Data
gromacs_ff
Trusted force field files for gromacs
lesSDRF
pydata-book
Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media
marioernestovaldes's Repositories
marioernestovaldes/gromacs_ff
Trusted force field files for gromacs
marioernestovaldes/AMBERff-in-NAMD
marioernestovaldes/AMRFinderPlus
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
marioernestovaldes/corals-lib-python
marioernestovaldes/datamapplot
Creating beautiful plots of data maps
marioernestovaldes/diamond
Accelerated BLAST compatible local sequence aligner.
marioernestovaldes/EIR
A toolkit for training deep learning models on genotype, tabular, sequence, image, array and binary data.
marioernestovaldes/gbdraw
A genome diagram generator for microbes
marioernestovaldes/gLM-genomic-language-model
Genomic language model predicts protein co-regulation and function
marioernestovaldes/IDSL.GOA
Gene Ontology Analysis for Metabolomics
marioernestovaldes/LP-PDBBind
marioernestovaldes/lrg-omics
marioernestovaldes/MOVE
MOVE (Multi-Omics Variational autoEncoder) for integrating multi-omics data and identifying cross modal associations
marioernestovaldes/NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
marioernestovaldes/panaroo
An updated pipeline for pangenome investigation
marioernestovaldes/patchworklib
Patchwork for matplotlib: A subplot manager for intuitive layouts in matplotlib, seaborn, and plotnine.
marioernestovaldes/PGBTR-GRN_Inference
PGBTR：A powerful and general method for inferring bacterial transcriptional regulatory networks
marioernestovaldes/pimms
Imputing proteomics data using deep learning models
marioernestovaldes/pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram)
marioernestovaldes/PyComplexHeatmap
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
marioernestovaldes/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
marioernestovaldes/PyWGCNA
PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
marioernestovaldes/quantms
Quantitative mass spectrometry workflow.
marioernestovaldes/QuEStVar_Manuscript
All the scripts and notebooks used to produce the data written in the manuscript titled "Statistical testing for protein equivalence identifies core functional modules conserved across 360 cancer cell lines and presents a general approach to investigating biological systems".
marioernestovaldes/scPROTEIN
marioernestovaldes/single-cell-transformer-papers
marioernestovaldes/Stabl
marioernestovaldes/statannotations
add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.
marioernestovaldes/TBtools-II
GUI/CommandLine Tool Box for biologistists to utilize NGS data.
marioernestovaldes/toolbox