Nesvilab/FragPipeTPP

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R
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Created 12 months ago
Updated 7 months ago

Nesvilab/FragPipeTPP

Nesvilab

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Enables FragPipe Ouput from (TPP workflow) to be made compatible with TPP-R package

FragPipe

A cross-platform proteomics data analysis suite

philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

MSBooster

MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring

IonQuant

A label free quantification tool.

PTM-Shepherd

A tool for summarizing open search results

TMT-Integrator

A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.

PD-Nodes

The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes

Crystal-C

Crystal-C: A computational tool for refinement of open search results

FragPipe-Analyst

An easy-to-use and interactive web application for FragPipe

FragPipeAnalystR

msconvert-scripts

Some shell scripts related to raw format conversion using msconvert

EntrapBench

Generate entrapment database and calculate false discovery proportion (FDP)

MSFragger-DIA-manuscript

Python and R scripts to generate the figures in the MSFragger-DIA paper

dia-umpire-gui

Simple one page java gui for DIA-Umpire

nesvilab.github.io

Nesvilab website