Slavov Laboratory

All

27 repositories

pSCoPE
Public
Prioritized Mass Spectrometry Proteomics. Prioritized Single-Cell ProtEomics by Mass Spectrometry code associated with the pSCoPE manuscript.
mass-spectrometry single-cell targeted-proteomics single-cell-analysis single-cell-proteomics bioinformatics
R
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MIT License
•1•4•0•0•Updated Dec 8, 2024Dec 8, 2024
QuantQC
Public
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.
quality-control mass-spectrometry omics sample-preparation single-cell-analysis single-cell-omics proteomics-data-analysis proteomi
HTML
•1•2•1•0•Updated Dec 2, 2024Dec 2, 2024
decode
Public
Computational pipeline for quantifying amino acid substitutions from alternate RNA decoding
translation sequencing proteomics
Jupyter Notebook
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Other
•0•0•0•0•Updated Nov 30, 2024Nov 30, 2024
CellPermeability
Public
Cell Permeability analysis
proteomics mass-spectrometry single-cell qc single-cell-analysis proteomics-data-analysis
R
•0•0•0•0•Updated Nov 5, 2024Nov 5, 2024
BayesPG
Public
Systematic inference of post transcriptional regulation using single cell protein and mRNA data
R
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MIT License
•0•0•0•0•Updated Oct 22, 2024Oct 22, 2024
early-stage-embryos
Public
Here you will find scripts and related files that are behind analyses presented in "Proteome asymmetry in mouse & human embryos before fate specification"".
developmental-biology embryo single-cell-proteomics
R
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MIT License
•0•0•0•0•Updated Sep 10, 2024Sep 10, 2024
plexDIA
Public
Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.
mass-spectrometry high-throughput single-cell proteomics-data-analysis multiplexed plexdia
R
•2•11•0•0•Updated Aug 19, 2024Aug 19, 2024
DO-MS
Public
An modular and extensible app for visualization of mass spectrometry data and optimization of data acquisition.
proteomics single-page-applications mass-spectrometry single-cell visulization proteomics-data-analysis
R
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MIT License
•10•26•5•12•Updated Jul 30, 2024Jul 30, 2024
Single-nucleus-proteomics
Public
Single-nucleus proteomics identifies regulators of protein transport
R
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MIT License
•1•0•0•0•Updated Jul 2, 2024Jul 2, 2024
EMT_TGFB_2023
Public
Dynamics of single-cell protein covariation during EMT. Analysis of TGF-B induced EMT in MCF10A cells using nPoP and SCoPE2.
emt single-cell-proteomics protein-covariation
R
•1•0•1•1•Updated Jun 17, 2024Jun 17, 2024
single_cell_oocyte
Public
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".
proteomics aging aging-biology oocytes
R
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MIT License
•0•0•0•0•Updated May 15, 2024May 15, 2024
oocyte_aging
Public
A code repository for the analysis of proteome changes associated with oocyte aging
R
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MIT License
•0•0•1•0•Updated Apr 13, 2024Apr 13, 2024
SC_Pancreas_KO
Public
Code or analysis in paper: An adult-restricted clock component links circadian rhythms to pancreatic β-cell maturation
R
•0•0•0•0•Updated Aug 7, 2023Aug 7, 2023
SCoPE2
Public
R
•6•17•0•11•Updated Jul 11, 2023Jul 11, 2023
SCP_recommendations
Public
Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. The code is distributed under an MIT license.
benchmarking proteomics benchmark-framework single-cell community-project proteomics-data-analysis
R
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MIT License
•4•10•5•0•Updated Apr 5, 2023Apr 5, 2023
DART-ID
Public
DART-ID: retention time alignment and peptide identification confidence updates
model software alignment proteomics mass-spectrometry bayesian-inference retention-time
Python
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MIT License
•4•15•4•4•Updated Feb 21, 2023Feb 21, 2023
plexDIA_perspective
Public
Strategies for increasing the depth and throughput of protein analysis by plexDIA. The code is distributed by an MIT license.
proteomics mass-spectrometry single-cell
MATLAB
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MIT License
•0•0•0•0•Updated Feb 4, 2023Feb 4, 2023
nPOP
Public
Code for the research article "Exploring functional protein covariation across single cells using nPOP". It is distributed under MIT license.
regulation gene-regulation proteomics sample-preparation single-cell-proteomics protein-complexes single-cell-ananlysis
R
•1•0•1•0•Updated Dec 27, 2022Dec 27, 2022
SPP
Public
Scripts and Pipelines for Proteomics are computational utilities for single-cell proteomics by mass spectrometry. The code is distributed by an MIT license.
mass-spectrometry single-cell pipline proteomics-data-integration proteomics-data-analysis
R
•0•0•0•0•Updated Nov 23, 2022Nov 23, 2022
isobaric-carrier
Public
R
•0•0•0•0•Updated Nov 7, 2022Nov 7, 2022
HIquant
Public
HIquant: An algorithm for quantifying homologous proteins and proteoforms from bottom-up mass-spec data
inference proteomics mass-spectrometry proteoforms proteomics-data-analysis
Python
•2•2•0•0•Updated Oct 16, 2022Oct 16, 2022
DO-MS-DIA
Public
HTML
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MIT License
•0•0•0•0•Updated Sep 8, 2022Sep 8, 2022
Adding_PMCID
Public
Adds PubMed Central IDs to latex bibliographies (bbl files) to ensure compatibility with NIH requirements.
Perl
•0•1•0•0•Updated Jun 28, 2020Jun 28, 2020
STLS
Public
Convex solver for structured total least squares problems
MATLAB
•2•4•0•0•Updated May 22, 2020May 22, 2020
tissue-ptr
Public
Code for analyzing post-transcriptional regulation across human tissues (Franks et al., 2017 DOI: 10.1371/journal.pcbi.1005535)
R
•2•3•0•0•Updated May 3, 2020May 3, 2020
ssGSEA2.0
Public
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
R
•79•0•0•0•Updated May 28, 2019May 28, 2019
DART-ID_2018
Public
Code for figures/data analysis of the DART-ID publication
Jupyter Notebook
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MIT License
•0•2•0•0•Updated May 15, 2019May 15, 2019