Single Cell — Community Home
This is a new, experimental "Community Home" for a given topic. It is intended to highlight community contributions over the years to a topic!2024 Year in Review
So many new additions to our community!
6
News
6
Events
2
Learning Pathways
4
Tutorials
2
Slides
5
Recordings
2
Faqs
7
Workflows
3
Contributors
News
- GTN's Gift for 2024
- 🖖🏾Galaxy SPOC Community: Year in Review
- SPOC CoFest 2024: How did it go?
- New Tutorial: Single-cell ATAC-seq standard processing with SnapATAC2
- From GTN Intern to Tutorial Author to Bioinformatician
- FAIR Data management in single cell analysis
Events
- 🖖🏾 SPOC II: the Write-a-Than
- Single-cell and sPatial Omics | Collaboration Fest
- 🖖🏾 SPOC Write-a-thon
- 2024 Bioinformatics Bootcamp - The Open University
- Galaxy Training Academy 2024
- FAIR data management in single-cell analysis
Learning Pathways
Tutorials
- GO Enrichment Analysis on Single-Cell RNA-Seq Data
- Single-cell ATAC-seq standard processing with SnapATAC2
- Filter, plot, and explore single cell RNA-seq data with Seurat
- Converting between common single cell data formats
Slides
Recordings
- Recording of Single-cell Formats and Resources
- Recording of Clustering 3K PBMCs with Scanpy
- Recording of Generating a single cell matrix using Alevin
- Recording of Importing files from public atlases
- Recording of Filter, plot and explore single-cell RNA-seq data with Scanpy (Python)
Faqs
- Using tutorial mode and the Case Study suite
- Why is my tool erroring as 'Above error raised while reading key '/layers' of type
from /.'
Workflows
- scRNA Plant Analysis
- Seurat Filter, Plot and Exlore tutorial
- GO Enrichment Workflow
- Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2
- AnnData to SingleCellExperiment (SCE) conversion
- AnnData to Seurat conversion
- AnnData to Cell Data Set (CDS) conversion
Contributors
2023 Year in Review
So many new additions to our community!
2
News
1
Learning Pathways
13
Tutorials
1
Slides
3
Recordings
3
Faqs
15
Workflows
2
Grants
2
Contributors
News
- Galaxy Single-cell Community: Year in Review
- Single cell subdomain re-launch: Unified and feedback-driven
Learning Pathways
Tutorials
- Converting NCBI Data to the AnnData Format
- Generating a single cell matrix using Alevin and combining datasets (bash + R)
- Inferring single cell trajectories with Scanpy
- Importing files from public atlases
- Filter, plot, and explore single cell RNA-seq data with Seurat (R)
- Filter, plot and explore single-cell RNA-seq data with Scanpy (Python)
- Scanpy Parameter Iterator
- Pre-processing of 10X Single-Cell ATAC-seq Datasets
- Inferring single cell trajectories with Monocle3 (R)
- Removing the effects of the cell cycle
- Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
- Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution
- Comparing inferred cell compositions using MuSiC deconvolution
Slides
Recordings
- Recording of Pre-processing of 10X Single-Cell RNA Datasets
- Recording of Combining single cell datasets after pre-processing
- Recording of Inferring single cell trajectories with Monocle3
Faqs
- Notebook-based tutorials can give different outputs
- How can I talk with other users?
- Use our Single Cell Omics Lab
Workflows
- EBI SCXA to AnnData (Scanpy) or Seurat Object
- NCBI to Anndata
- Inferring Trajectories with Scanpy Tutorial Workflow
- Clustering 3k PBMC with Scanpy
- Scanpy Parameter Iterator workflow full (imported from URL)
- Filter, Plot and Explore Single-cell RNA-seq Data updated
- Preprocessing of 10X scRNA-seq data
- Trajectory analysis using Monocle3 - full tutorial workflow
- scATAC-seq FASTQ to Count Matrix
- scATAC-seq Count Matrix Filtering
- Cell Cycle Regression Workflow
- MuSiC-Deconvolution: Compare
- MuSiC-Deconvolution: Data generation | bulk | ESet
- MuSiC-Deconvolution: Data generation | sc | metadata
- MuSiC-Deconvolution: Data generation | sc | matrix + ESet
Grants
Contributors
2022 Year in Review
So many new additions to our community!
2
News
4
Tutorials
1
Slides
9
Faqs
3
Workflows
1
Grants
4
Contributors
News
- New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation!
- New Topic: Single Cell Analysis!
Tutorials
- Inferring single cell trajectories with Monocle3
- Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin
- Combining single cell datasets after pre-processing
- Bulk RNA Deconvolution with MuSiC
Slides
Faqs
- How do I know what protocol my data was sequenced with?
- Why is Alevin is not working?
- The UMAP Plots errors out sometimes?
- Are Barcodes always on R1 and Sequence data on R2?
- AnnData Import/ AnnData Manipulate not working?
- On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc.
- On Scanpy PlotEmbed, the tool is failing
- My Scanpy FindMarkers step is giving me an empty table
- Why is Alevin is not working?
Workflows
Grants
Contributors
2021 Year in Review
So many new additions to our community!
1
News
6
Tutorials
3
Slides
10
Recordings
6
Faqs
4
Workflows
3
Contributors
News
Tutorials
- Filtrado, representación y exploración de secuenciación de ARN de células únicas
- Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin
- Analysis of plant scRNA-Seq Data with Scanpy
- Inferring single cell trajectories with Scanpy (Python)
- Filter, plot and explore single-cell RNA-seq data with Scanpy
- Generating a single cell matrix using Alevin
Slides
- Una introducción al análisis de datos scRNA-seq
- Introducción al análisis de datos de scRNA-seq
- An introduction to scRNA-seq data analysis
Recordings
- Recording of Understanding Barcodes
- Recording of Pre-processing of 10X Single-Cell RNA Datasets
- Recording of Clustering 3K PBMCs with Scanpy
- Recording of Bulk RNA Deconvolution with MuSiC
- Recording of Inferring single cell trajectories with Scanpy (Python)
- Recording of An introduction to scRNA-seq data analysis
- Recording of Generating a single cell matrix using Alevin
- Recording of Analysis of plant scRNA-Seq Data with Scanpy
- Recording of Combining single cell datasets after pre-processing
- Recording of Filter, plot and explore single-cell RNA-seq data with Scanpy
Faqs
- Are UMIs not actually unique?
- Why do we only consider highly variable genes?
- Can RNA-seq techniques be applied to scRNA-seq?
- What exactly is a ‘Gene profile’?
- Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?
- Why is amplification more of an issue in scRNA-seq than RNA-seq?
Workflows
- scRNA Plant Analysis
- CS3_Filter, Plot and Explore Single-cell RNA-seq Data
- Combining datasets after pre-processing
- Generating a single cell matrix using Alevin
Contributors
2020 Year in Review
So many new additions to our community!
2
Slides
1
Recordings
3
Contributors
2019 Year in Review
So many new additions to our community!
6
Tutorials
1
Slides
4
Workflows
4
Contributors
2018 Year in Review
So many new additions to our community!
3
Contributors
Contributors
2017 Year in Review
So many new additions to our community!
12
Contributors
Cumulative Data as CSV
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