Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
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Sep 16, 2026 - Nextflow
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lfq
Here are 10 public repositories matching this topic...
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
workflow pipeline nextflow proteomics dia mass-spectrometry openms proteogenomics tmt nf-core mass-spec lfq
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May 6, 2024 - Nextflow
An open-source Python package for accurate and sensitive peptide and protein quantification.
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Aug 21, 2026 - Python
A comprehensive R package for label-free proteomics data analysis and modeling
machine-learning r modeling rstats proteomics mass-spectrometry r-package differential-expression biomarkers lfq
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May 7, 2026 - R
pipeline for TMT/LFQ proteomics: QC, volcano plots, and Reactome enrichment
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Oct 2, 2025
Label-free DDA proteomics differential abundance analysis, benchmarked against a spike-in study with known ground truth and applied to an arginine transporter knockout in Francisella tularensis.
bioinformatics r computational-biology bioconductor proteomics dda mass-spectrometry maxquant false-discovery-rate label-free-quantification mixed-models robust-regression qfeatures lfq differential-abundance bacterial-pathogenesis msqrob2 spike-in-benchmark pseudo-replication francisella-tularensis
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Sep 18, 2026 - R
Reanalysis of Phaeodactylum tricornutum nitrogen-starvation proteome (PRIDE PXD033328, MaxQuant LFQ): cleaning + Perseus imputation, PCA/PLS-DA, differential proteins, on/off switch theme. Full R.
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Jun 15, 2026 - R
Missing-value imputation benchmark for peptide-level LFQ proteomics. Evaluated on a spike-in dataset and via simulation.
python imputation proteomics dia mass-spectrometry label-free-quantification limma missing-values lfq questvar
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Mar 22, 2026 - Jupyter Notebook
🔍 Optimize multi-objective tasks with Tchebycheff scalarization for better alignment and efficient Pareto frontier exploration.
python syntax-highlighting space color-scheme topic-modeling proteomics labeling mass-spectrometry text-processing tmtheme ccsds msstats ecss tmt cs2 tmt-data-analysis pus-standard lfq
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Sep 18, 2026 - Python
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