Colliton/Code-storage

"This repository contains Python scripts for biological data analysis, including Kaplan-Meier survival analysis, volcano plots for gene expression analysis, heatmaps for immune cell infiltration in murine models treated with Pyrvinium Pamoate, and SQL queries for data extraction and preprocessing."

Language: Jupyter Notebook - Size: 2.81 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

xieguigang/mzkit

Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS and GC-MS raw data, chemoinformatics data analysis and data visualization.

Language: Visual Basic .NET - Size: 504 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 60 - Forks: 17

eugenemel/maven

Maven GUI: Metabolomics Analysis and Visualization Engine

Language: C++ - Size: 5.64 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 20 - Forks: 10

TT2DR-StenoDiabetesCenterCopenhagen/COFstudy_AdiposeSerum_Multi-Omics

Detrimental effects of carbohydrate overfeeding of non-obese early middle-aged low birthweight men with and without non-alcoholic fatty liver disease (NAFLD) based on fasting serum samples and adipose tissue biopsies.

Size: 141 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

RDA-MOMSI/Dashboard

MOMSI WG Landscape Review Dashboard

Language: JavaScript - Size: 5.42 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 1 - Forks: 0

CPM-Metabolomics-Lipidomics/soda-light

This is a lipidomics only version of iSODA from NDCN.

Language: R - Size: 167 MB - Last synced at: 8 days ago - Pushed at: 18 days ago - Stars: 1 - Forks: 1

lifs-tools/goslin-webapp

Web application and REST Api for parsers for the Grammars on succinct lipid nomenclature (Goslin).

Language: Java - Size: 1.31 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 1 - Forks: 0

SLINGhub/midar

Small Molecule Mass Spectrometry Data Post-Processing, Quality Control, Exploration and Reporting

Language: R - Size: 1.22 GB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 7 - Forks: 0

InnovativeOmics/Core-Match

Core scripts for FluoroMatch, LipidMatch, and PolyMatch

Language: R - Size: 19.6 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 2 - Forks: 1

BioinfOMICS/LipidSigR

R package for Analyzing Lipidomic Datasets

Language: R - Size: 101 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 0

idslme/IDSL_MINT

A Deep Learning Framework to Interpret Raw Mass Spectrometry (m/z) Data

Language: Python - Size: 972 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 20 - Forks: 1

octopode/seelipids

Making patterns visible in complex lipidomic data

Language: R - Size: 11 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

KacperKaszuba0608/OCIAD1-Analysis

OCIAD1 Analysis

Language: R - Size: 56.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

saezlab/lipyd

Python module for lipidomics LC MS/MS data analysis

Language: Python - Size: 17.9 MB - Last synced at: about 2 months ago - Pushed at: 11 months ago - Stars: 15 - Forks: 3

lifs-tools/goslin

Goslin is the Grammar on succinct lipid nomenclature.

Language: ANTLR - Size: 7.34 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 11 - Forks: 2

nara3m/nara3m

Nara Marella

Size: 80.1 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

ahmohamed/lipidr

Data Mining and Analysis of Lipidomics datasets in R

Language: R - Size: 50.6 MB - Last synced at: 25 days ago - Pushed at: almost 2 years ago - Stars: 30 - Forks: 14

2n3m/2n3m

Biomedicine, Pharma, Life Science, IT Consulting

Size: 82 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

M3Metabolomics/MetaboLink

Repository for metabolomics and lipidomics data processing app.

Language: R - Size: 23.1 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 3 - Forks: 3

ricoderks/lipidomics

A shiny app for my lipidomics workflow.

Language: R - Size: 2.42 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

lifs-tools/.github

LIFS Tools Overview

Size: 39.1 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

systemsomicslab/ms2lipid

MS2Lipid is a lipid subclass prediction program using machine learning and curated tandem mass spectral data.

Language: Jupyter Notebook - Size: 5.87 MB - Last synced at: 16 days ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

lsmsgeneva/MsRadaR

MsRadaR, A Tool for De-Novo Structural Elucidation of Lipids from MS/MS Spectra (EDP-CID, EAD)

Language: R - Size: 2.49 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

lifs-tools/pygoslin

Python implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).

Language: Python - Size: 9.75 MB - Last synced at: 11 days ago - Pushed at: 10 months ago - Stars: 4 - Forks: 2

lifs-tools/awesome-lipidomics

A collection of awesome lipidomics tools and resources

Size: 63.5 KB - Last synced at: 24 days ago - Pushed at: almost 3 years ago - Stars: 12 - Forks: 2

Hartviger/M.Sc.-optimization-of-B.sc-project

Upadtes to B.sc. project, creating a lipid heatmap for lipidomics data. Read further on bio on B.Sc. programs.

Language: R - Size: 4.55 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

lifs-tools/cppgoslin

C++ implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).

Language: C++ - Size: 9.19 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

idslme/IDSL.IPA

Intrinsic Peak Analysis (IPA) pipeline for peak-picking in large-scale untargeted small molecule analysis including metabolomics, lipidomics, exposomics, and environmental studies.

Language: R - Size: 17.1 MB - Last synced at: 7 days ago - Pushed at: almost 2 years ago - Stars: 13 - Forks: 1

idslme/IDSL.UFA

United Formula Annotation (UFA) for LC-HRMS data

Language: R - Size: 3.17 MB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 1

syjgino/SLA

A DMS Shotgun Lipidomics Workflow Application to Facilitate High-Throughput, Comprehensive Lipidomics

Size: 312 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 4 - Forks: 3

eagomezc/Machine-Learning-and-RA-treatment

This repository contains the script used to study blood pro-resolving mediators as biomarkers to predict the response of DMARD treatment in rheumatoid arthritis patients

Language: R - Size: 34.2 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

zybinmikhail/Thesis

Machine Learning Based Analysis of Gene Expression and Lipid Composition of the Schizophrenia Brain

Language: Jupyter Notebook - Size: 117 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

pnnl/IonToolPack

A software tool for omics-agnostic automated quality control of mass spectrometry data.

Language: Python - Size: 687 MB - Last synced at: 2 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1

Hartviger/B.Sc._programs

My B.Sc. project involves a collaboration with the M3 Lab Group at SDU. The purpose is to create a Shiny app that will be published. My code will be used in the app to visualize and analysis Metabolomics, Lipidomics data.

Language: R - Size: 2.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

lifs-tools/jgoslin

Java implementation of the latest shorthand nomenclature.

Language: Java - Size: 18.9 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 0

octopode/homeocurvature-2024

Data, scripts, and figures for "Homeocurvature adaptation of phospholipids to pressure in deep-sea invertebrates"

Language: R - Size: 384 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

Hartviger/B.Sc.-programs

My B.Sc. project involves a collaboration with the M3 Lab Group at SDU. The purpose is to create a Shiny app that will be published. My code will be used in the app to visualize and analysis Metabolomics, Lipidomics data.

Size: 0 Bytes - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

EMSL-Computing/IonToolPack

A software tool for omics-agnostic automated quality control of mass spectrometry data.

Language: Python - Size: 460 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

EuBIC/ReproducibleMSGuidelines

This project aims at defining a set of guidelines for reproducible mass spectrometry-based experiments.

Language: JavaScript - Size: 332 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 1

idslme/IDSL.MXP

A light weight and fast parser for reading mzML, mzXML and netCDF data files

Language: R - Size: 199 KB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 0

Harel-lab/APRT-sex-differences

Language: Jupyter Notebook - Size: 27.4 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

lifs-tools/rmzTab-m

The R-language bindings for mzTab-M

Language: R - Size: 2.04 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

barupal/ADNI

Alzheimer's Disease Neuroimaging Initiative: Untargeted Lipidomics Analysis

Language: R - Size: 18.6 KB - Last synced at: about 1 month ago - Pushed at: over 6 years ago - Stars: 6 - Forks: 1

computational-metabolomics/dimspy-galaxy

Galaxy tools for Python package DIMSpy: data processing of Direct-Infusion Mass Spectrometry-based metabolomics and lipidomics data

Size: 14.8 MB - Last synced at: 7 months ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 4

pyQms/pyqms

pyQms, generalized, fast and accurate mass spectrometry data quantification

Language: Python - Size: 1.93 MB - Last synced at: 18 days ago - Pushed at: 11 months ago - Stars: 28 - Forks: 9

respiratory-immunology-lab/metabolome-lipidome-MSDIAL

Guide to processing raw LCMS metabolomic and lipidomic data using MS-DIAL, followed by data pre-processing and secondary annotation (of metabolites) in R.

Language: R - Size: 37.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 4

SysMedOs/LipidLynxX

LipidLynxX provides the possibility to convert, cross-match, and link various lipid annotations to the tools supporting lipid ontology, pathway, and network analysis aiming systems-wide integration and functional annotation of lipidome dynamics in health and disease.

Language: Python - Size: 15.9 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 6

IPHYS-Bioinformatics/LORA

LORA: Lipid Over-Representation Analysis

Language: Python - Size: 18.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

SysMedOs/StarCats

epilipidomics tools for Lipostar 2 developed by Team SysMedOs

Size: 98.6 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

GarrettLab-UF/LipidMatch-Normalizer

Quantify lipids using a feature table and internal standards table

Language: R - Size: 72.3 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 2

wenbostar/metaX

metaX: a flexible and comprehensive software for processing omics data.

Language: R - Size: 51.2 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 14 - Forks: 12

ricoderks/QComics

Shiny app to have a look at the quality of -omics data.

Language: R - Size: 83 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

SLINGhub/iSLS9 📦

iSLS9 data analysis workshop

Language: R - Size: 9.63 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 1

SLINGhub/iSLS11

Scripts and notes used in the iSLS11 workshop on data analysis

Language: HTML - Size: 35.3 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

ptogias/rf-lipidomics

Addressing n<<p biology problems with interpretable random forest results via partial dependence plots. - Construction of an ideal high-density lipoprotein

Size: 2.74 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

LewisLabUCSD/iLipidome

iLipidome is a novel lipidomic data analysis framework.

Language: R - Size: 43.9 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

SysBioChalmers/SLIMEr

Collection of scripts for improving lipid constraints in yeast-GEM

Language: MATLAB - Size: 6.17 MB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 1

SLINGhub/LICAR

Functions and a Shiny app to correct class-based separation LC-MRM-MS lipidomics data for isotopic interferences

Language: R - Size: 3.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 2

SLINGhub/iSLS10

iSLS10 data analysis workshop

Language: R - Size: 8.82 MB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 2

bshashikadze/diabetes-lung-omics-paper

Reproducibility repo for Shashikadze et al. "Multi-omics profiling of lungs from genetically diabetic pigs reveals reduced ALOX15 levels and impaired eicosanoid switching as mechanisms contributing to a proinflammatory milieu".

Language: Markdown - Size: 426 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

ShinyFabio/ADViSELipidomics

ADViSELipidomics is a novel Shiny app for the preprocessing, analysis, and visualization of lipidomics data.

Language: R - Size: 4.82 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0

SLINGhub/SLINGtools

Facilitate lipidomics data analysis in R

Language: R - Size: 18.9 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

lifs-tools/rgoslin-old 📦

R implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).

Language: C++ - Size: 9.93 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

vanmooylipidomics/LOBSTAHS

Git repository for the R package "LOBSTAHS" (Lipid and Oxylipin Biomarker Screening Through Adduct Hierarchy Sequences)

Language: R - Size: 32.4 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 12

idslme/IDSL.UFAx

Exhaustive Formula Annotation from ions to formula

Language: R - Size: 7 MB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

RayLabIIITD/pyLFDA

pyLFDA is a tool which allows analysis of pairwise lipid force distribution along with other functions such as curvature and diffusion.

Language: Jupyter Notebook - Size: 88.6 MB - Last synced at: 12 days ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

Khrameeva-Lab/lipidomics_analysis_2021 📦

The Hitchhiker’s Guide to untargeted lipidomics analysis: Practical guidelines

Language: R - Size: 2.95 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

SysMedOs/lipidhunter

LipidHunter is capable to perform bottom up identification of lipids from LC-MS/MS and shotgun lipidomics data by resembling a workflow of manual spectra annotation. LipidHunter generates interactive HTML output with its unique six-panel-image, which provides an easy way to review, store, and share the identification results.

Language: Python - Size: 32.6 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 6

SLINGhub/RwithSLING

RwithSLING notes

Language: TeX - Size: 10.3 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

SysMedOs/AdipoAtlasScripts

Python & R scripts collection for AdipoAtlas project

Language: Python - Size: 14.9 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

SysMedOs/epiLION

epiLipidome Identifier and Optimized Nomenclature

Language: Python - Size: 1.53 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 2

SLINGhub/Manuscript_Sieber-Ruckstuhl_Burla_2019

R scipts used for manuscript Sieber-Ruckstuhl, Burla, et al. (2019) Changes in the Canine Plasma Lipidome after Short- and Long-Term Excess Glucocorticoid Exposure'

Language: R - Size: 104 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 2

cpanse/cosmiq

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/cosmiq.html Contributions: http://www.bioconductor.org/packages/devel/bioc/html/cosmiq.html. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=cosmiq.

Language: R - Size: 27.3 KB - Last synced at: about 2 months ago - Pushed at: over 9 years ago - Stars: 0 - Forks: 0

lwjohnst86/ada.2017

Abstract and Presentation Files for ADA 2017

Language: R - Size: 14.6 KB - Last synced at: 6 days ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

ginkgobioworks/xcms Fork of benjiec/xcms

Ginkgo Bioworks' extensions and fixes to XCMS

Language: R - Size: 343 KB - Last synced at: about 1 month ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0