18 skills found
vdemichev / Diann RpackageReport processing and protein quantification for MS-based proteomics
fgcz / ProlfquaDifferential Expression Analysis tool box R lang package for omics data
yxnyu / SakePPQuantifying Protein-Protein Interaction with a Spatial Attention Kinetic Graph Neural Network
tvpham / IqAn R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
microsoft / Protein UqBenchmarking uncertainty quantification methods on proteins.
MannLabs / AlphaquantAn open-source Python package for accurate and sensitive peptide and protein quantification.
CapraLab / CosmisCOSMIS is a framework for quantifying the mutational constraint on amino acid sites in 3D spatial neighborhoods. The framework currently maps the landscape of 3D mutational constraint on 6.1 amino acid sites covering >80% (16,533) of human proteins.
Shen-Lab / BALBayesian Active Learning for Optimization and Uncertainty Quantification with Applications to Protein Docking
biospi / BayesprotDEPRECATED - Bayesian linear mixed-effects model for protein-level quantification in proteomics
EraslanBas / HumanTransProtThis repository contains the data preprocessing analysis scripts of the manuscript "Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues" by Eraslan et al., Molecular Systems Biology, 2019
SynPuCo / SynapseCounterSynapse Counter plug-in for ImageJ, developed by Egor Dzyubenko and Andrey Rozenberg, is a helpful scientific tool designed for synapse formation studies. It is developed for rapid, automatic, unbiased quantification of synaptic puncta revealed by synaptic marker proteins fluorescence.
Weeks-UNC / DeltaSHAPESHAPE-MaP both measures RNA flexibility at single-nucleotide resolution and quantifies the uncertainties in these measurements. The deltaSHAPE framework incorporates these uncertainties to allow detection of RNA structural differences between any two states, including the general effect of the cellular environment, protein binding in cells, and pathway-dependent RNA conformational changes.
CompOmics / ReporterProtein quantification based on reporter ions
biosustain / AutoprotThe autoprot pipeline allows for absolute quantification of proteins from raw mass-spectrometry files in an automated manner.
LFAQ / LFAQa novel algorithm for label-free absolute protein quantification
PNNL-Comp-Mass-Spec / InfernoRDNInfernoRDN can perform various downstream analyses on large scale datasets from proteomics and microarrays
mjohn218 / StoichiometricBalanceGiven 1) a protein interaction network, with interfaces resolved and 2) Copy numbers for some of the proteins, Quantify degree of stoichiometric balance in protein copy numbers
proteomicsyates / PINTPINT is a new comprehensive web-based system to store, visualize, and query experimental proteomics data obtained under different experimental conditions and projects. PINT provides a very powerful query system through the use of different proteomics-specific data query commands running over both the experimental features and external annotations of the detected protein lists (such as UniprotKB).
