marioernestovaldes Goto Github PK

pgbtr-grn_inference

PGBTR：A powerful and general method for inferring bacterial transcriptional regulatory networks

picked_group_fdr

Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments

pimms

Imputing proteomics data using deep learning models

proteomics-tutorial

pycirclize

Circular visualization in Python (Circos Plot, Chord Diagram)

pycomplexheatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

pydata-book

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media

pydeseq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

pygenomeviz

A genome visualization python package for comparative genomics

pylipid

A python toolkit for analysing membrane protein-lipid interactions.

pywgcna

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)

quantms

Quantitative mass spectrometry workflow.

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".

rayshader

R Package for 2D and 3D mapping and data visualization

sage-proteomics

Proteomics search & quantification so fast that it feels like magic

scienceplots

Matplotlib styles for scientific plotting

scprotein

sds375

SDS 375 Data Visualization in R

sepepquant

SEPepQuant: a graph theory-based approach enables comprehensive protein isoform characterization in shotgun proteomics

single-cell-transformer-papers

stabl

staphopia-sccmec

A standalone version of Staphopia's SCCmec typing method.

statannotations

add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.

sumd-analyzer

Analysis script for SuMD trajectories

tbtools-ii

GUI/CommandLine Tool Box for biologistists to utilize NGS data.

thermorawfileparser

Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono

tmt_analysis_examples

Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.

toolbox

treemmer

Python tool to reduce size and redundancy of phylogenetic datasets

tsne-embedding

Embedding to Reference t-SNE Space Addresses Batch Effects in Single-Cell Classification