Slavov Laboratory

DO-MS

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

SCoPE2

DART-ID

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

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.

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)

HIquant

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

Adding_PMCID

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

DART-ID_2018

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

DO-MS-DIA

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.

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.

SC_Pancreas_KO

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

SPP

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

ssGSEA2.0

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