Application of the LoRAS oversampling approach on single-cell/single-nuclei data to annotate/identify specific cell populations in new data based on previously, manually curated data.
SEEK ID: https://fairdomhub.org/assays/1368
Modelling Analysis
Projects: iRhythmics
Investigation: hidden item
Study: hidden item
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Biological problem addressed: Annotation
Organisms: No organisms
- Data and Jupyter notebooks for our analysis on Glial cell detection
- Data and Jupyter notebooks for our analysis on Proliferative Cardiomyocyte detection
- R script for scSynO usage of the Allen Brain Atlas data
- R script to generate the preprocessing input for scSynO
- Unix script for the kallisto bustools processing of scRNA-seq data
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Created: 16th Oct 2020 at 13:12
Last updated: 7th May 2021 at 15:07
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Projects that do not fall under current programmes.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity
Web page: Not specified
The project addresses the generation and establishment of programmed pacemaker cells for an in vitro drug testing possibility to perform predictive tests. This may lead to an improved treatment of cardiac arrhythmias or an accurate identification of potential drug molecules at a very early stage of development. Important benefits will arise in verifying the safety of a wide variety of medicines while reducing animal testing. For more information you may visit our project website at ...
Programme: Independent Projects
Public web page: https://irhythmics.med.uni-rostock.de/
Organisms: Homo sapiens, Mus musculus
Visualization of the workflow demonstrating a step-by-step explanation for a sc-SynO analysis. a) Several or one snRNA-Seq or scRNA-Seq fastq datasets can be used as an input. Here, we identify our cell population of interest and provide raw or normalized read counts of this specific population to sc-SynO for training. b) Further information for cluster annotation and processed count data are serving as input for the core algorithm. c) Based on the data input, we utilize the LoRAS synthetic ...
Investigations: 1 hidden item
Studies: 1 hidden item
Validation of the sc-SynO model for the first use case of cardiac glial cell annotation. UMAP representation of the manually clustered Bl6 dataset of Wolfien et al. (2020) Precicted cells of sc-SynO are highlighted in blue, cells not chosen are grey. UMAP representation of the manually clustered dataset of Vidal (2019). Precicted cells of sc-SynO are highlighted in blue, cells not chosen are grey. Average expression of the respective top five cardiac glial cell marker genes for both validation ...
Investigations: 1 hidden item
Studies: 1 hidden item
Validation of the sc-SynO model for the second use case of proliferative cardiomyocytes annotation. a) UMAP representation of the manually clustered single-nuclei dataset of Linscheid et al. (2019) Precicted cells of sc-SynO are highlighted in blue (based on top 20 selected features in the training model), red (based on top 100 selected features in the training model) cells not chosen are grey. b) UMAP representation of the manually clustered dataset of Vidal et al. (2020). PPrecicted cells of ...
Investigations: 1 hidden item
Studies: 1 hidden item
Here, we describe the index file generation of the mm10 genome, the genome alignment with kallisto, and quantification with bustools to obtain the used spliced / unspliced transcript input.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Here is the detailed R script to generate the input needed by scSynO for synthetic cell generation and classification model training.
The code that can be embedded into any other Seurat data processing workflow is:
cell_expression_target_cluster <- as.matrix(GetAssayData(seuratobject, slot = "data")[, WhichCells(seuratobject, ident = "target_cluster_number")]) cell_expression_all_other_clusters <- as.matrix(GetAssayData(seuratobject, slot = "data")[, WhichCells(seuratobject, ident = ...
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Single nuclei transcriptomics data as .csv files from the Allen Brain atlas data set of mus musculus (https://celltypes.brain-map.org/) have been utilized as an input for scSynO. The underlying analysis is part of the manuscript entitled "Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling". Data anaylsis and visalizations were mainly generated with the Seurat R package (https://satijalab.org/seurat/archive/v3.2/spatial_vignette.html)
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Saptarshi Bej
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Saptarshi Bej
Submitter: Saptarshi Bej
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: 1 hidden item
Studies: 1 hidden item