Slavov Laboratory's Projects
Adds PubMed Central IDs to latex bibliographies (bbl files) to ensure compatibility with NIH requirements.
Cell Permeability analysis
DART-ID: retention time alignment and peptide identification confidence updates
Code for figures/data analysis of the DART-ID publication
An modular and extensible app for visualization of mass spectrometry data and optimization of data acquisition.
Dynamics of single-cell protein covariation during EMT. Analysis of TGF-B induced EMT in MCF10A cells using nPoP and SCoPE2.
HIquant: An algorithm for quantifying homologous proteins and proteoforms from bottom-up mass-spec data
Code for the research article "Exploring functional protein covariation across single cells using nPOP". It is distributed under MIT license.
A code repository for the analysis of proteome changes associated with oocyte aging
Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.
Strategies for increasing the depth and throughput of protein analysis by plexDIA. The code is distributed by an MIT license.
Prioritized Mass Spectrometry Proteomics. Prioritized Single-Cell ProtEomics by Mass Spectrometry code associated with the pSCoPE manuscript.
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.
Code or analysis in paper: An adult-restricted clock component links circadian rhythms to pancreatic β-cell maturation
Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. The code is distributed under an MIT license.
Single-nucleus proteomics identifies regulators of protein transport
Scripts and Pipelines for Proteomics are computational utilities for single-cell proteomics by mass spectrometry. The code is distributed by an MIT license.
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
Convex solver for structured total least squares problems
Code for analyzing post-transcriptional regulation across human tissues (Franks et al., 2017 DOI: 10.1371/journal.pcbi.1005535)