Slavov Laboratory

DO-MS

An modular and extensible app for visualization of mass spectrometry data and optimization of data acquisition.

DART-ID

DART-ID: retention time alignment and peptide identification confidence updates

SCoPE2

plexDIA

Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.

SCP_recommendations

Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. The code is distributed under an MIT license.

QuantQC

QuantQC is a package for quality control (QC) of single-cell proteomics data. It is optimized to work with nPOP, a method for massively parallel sample preparation on glass slides.

STLS

Convex solver for structured total least squares problems

pSCoPE

Prioritized Mass Spectrometry Proteomics. Prioritized Single-Cell ProtEomics by Mass Spectrometry code associated with the pSCoPE manuscript.

tissue-ptr

Code for analyzing post-transcriptional regulation across human tissues (Franks et al., 2017 DOI: 10.1371/journal.pcbi.1005535)

CellPermeability

Cell Permeability analysis

HIquant

HIquant: An algorithm for quantifying homologous proteins and proteoforms from bottom-up mass-spec data

DART-ID_2018

Code for figures/data analysis of the DART-ID publication

Protein-Clearance

Analysis from Leduc and Slavov (2025): Protein degradation and growth dependent dilution substantially shape mammalian proteomes

sc_metabolic_pulse

Analysis from in vivo single cell metabolic pulse chase analysis

Adding_PMCID

Adds PubMed Central IDs to latex bibliographies (bbl files) to ensure compatibility with NIH requirements.

decode

Computational pipeline for quantifying amino acid substitutions from alternate RNA decoding

Single-nucleus-proteomics

Single-nucleus proteomics identifies regulators of protein transport

SPP

Scripts and Pipelines for Proteomics are computational utilities for single-cell proteomics by mass spectrometry. The code is distributed by an MIT license.

BayesPG

Systematic inference of post transcriptional regulation using single cell protein and mRNA data

DO-MS-DIA

early-stage-embryos

Here you will find scripts and related files that are behind analyses presented in "Proteome asymmetry in mouse & human embryos before fate specification"".

EMT_TGFB_2023

Dynamics of single-cell protein covariation during EMT. Analysis of TGF-B induced EMT in MCF10A cells using nPoP and SCoPE2.

isobaric-carrier

nPOP

Code for the research article "Exploring functional protein covariation across single cells using nPOP". It is distributed under MIT license.

oocyte_aging

A code repository for the analysis of proteome changes associated with oocyte aging

plexDIA_perspective

Strategies for increasing the depth and throughput of protein analysis by plexDIA. The code is distributed by an MIT license.

SC_Pancreas_KO

Code or analysis in paper: An adult-restricted clock component links circadian rhythms to pancreatic β-cell maturation

single_cell_oocyte

Here you will find scripts and related files that are behind analyses presented in "Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes".

ssGSEA2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)