Single cell — Monthly Updates

📰 News

• New Tutorial: Single-cell ATAC-seq standard processing with SnapATAC2 (July 12, 2024)

📚 Tutorials

• Single-cell ATAC-seq standard processing with SnapATAC2 (July 11, 2024)

🖼️ Slides

• Single-cell Formats and Resources (July 26, 2024)

🛠️ Workflows

• Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2 (July 11, 2024)

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📰 News

• From GTN Intern to Tutorial Author to Bioinformatician (June 13, 2024)

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📚 Tutorials

• Filter, plot, and explore single cell RNA-seq data with Seurat (April 09, 2024)

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📚 Tutorials

• Converting between common single cell data formats (February 13, 2024)

🛠️ Workflows

• AnnData to SingleCellExperiment (SCE) conversion (February 13, 2024)
• AnnData to Seurat conversion (February 13, 2024)
• AnnData to Cell Data Set (CDS) conversion (February 13, 2024)

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📰 News

• Galaxy Single-cell Community: Year in Review (December 22, 2023)

📚 Tutorials

• Converting NCBI Data to the AnnData Format (December 13, 2023)
• Generating a single cell matrix using Alevin and combining datasets (bash + R) (December 08, 2023)
• Inferring single cell trajectories with Scanpy (December 08, 2023)

🛠️ Workflows

• EBI SCXA to AnnData (Scanpy) or Seurat Object (December 14, 2023)
• NCBI to Anndata (December 13, 2023)
• Inferring Trajectories with Scanpy Tutorial Workflow (December 08, 2023)
• Clustering 3k PBMC with Scanpy (December 05, 2023)

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📚 Tutorials

• Importing files from public atlases (November 14, 2023)

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📚 Tutorials

• Filter, plot, and explore single cell RNA-seq data with Seurat (R) (October 02, 2023)

❓ Faqs

• Notebook-based tutorials can give different outputs (October 17, 2023)
• How can I talk with other users? (October 08, 2023)
• Use our Single Cell Omics Lab (October 08, 2023)

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🖼️ Slides

• Automated Cell Annotation (September 04, 2023)

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📚 Tutorials

• Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) (August 25, 2023)

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📚 Tutorials

• Scanpy Parameter Iterator (July 19, 2023)

🛠️ Workflows

• Scanpy Parameter Iterator workflow full (imported from URL) (July 19, 2023)

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🛠️ Workflows

• Filter, Plot and Explore Single-cell RNA-seq Data updated (June 13, 2023)

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🛠️ Workflows

• Preprocessing of 10X scRNA-seq data (May 19, 2023)
• Trajectory analysis using Monocle3 - full tutorial workflow (May 16, 2023)

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📚 Tutorials

• Pre-processing of 10X Single-Cell ATAC-seq Datasets (April 24, 2023)
• Inferring single cell trajectories with Monocle3 (R) (April 12, 2023)

🛠️ Workflows

• scATAC-seq FASTQ to Count Matrix (April 24, 2023)
• scATAC-seq Count Matrix Filtering (April 24, 2023)

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📚 Tutorials

• Removing the effects of the cell cycle (January 25, 2023)
• Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution (January 20, 2023)
• Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution (January 20, 2023)
• Comparing inferred cell compositions using MuSiC deconvolution (January 20, 2023)

🛠️ Workflows

• Cell Cycle Regression Workflow (January 25, 2023)
• MuSiC-Deconvolution: Compare (January 20, 2023)
• MuSiC-Deconvolution: Data generation | bulk | ESet (January 20, 2023)
• MuSiC-Deconvolution: Data generation | sc | metadata (January 20, 2023)
• MuSiC-Deconvolution: Data generation | sc | matrix + ESet (January 20, 2023)

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📰 News

• New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation! (November 29, 2022)
• New Topic: Single Cell Analysis! (November 18, 2022)

❓ Faqs

• How do I know what protocol my data was sequenced with? (November 18, 2022)

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📚 Tutorials

• Inferring single cell trajectories with Monocle3 (September 30, 2022)
• Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin (September 08, 2022)
• Combining single cell datasets after pre-processing (September 08, 2022)

🖼️ Slides

• Trajectory analysis (September 30, 2022)

❓ Faqs

• Why is Alevin is not working? (September 08, 2022)

🛠️ Workflows

• Monocle3 workflow (September 30, 2022)
• AnnData object to Monocle input files (September 30, 2022)

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❓ Faqs

• The UMAP Plots errors out sometimes? (March 02, 2022)
• Are Barcodes always on R1 and Sequence data on R2? (March 02, 2022)
• AnnData Import/ AnnData Manipulate not working? (March 02, 2022)

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📚 Tutorials

• Bulk RNA Deconvolution with MuSiC (February 11, 2022)

❓ Faqs

• On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc. (February 28, 2022)
• On Scanpy PlotEmbed, the tool is failing (February 28, 2022)
• My Scanpy FindMarkers step is giving me an empty table (February 28, 2022)
• Why is Alevin is not working? (February 28, 2022)

🛠️ Workflows

• MuSiC Workflow (February 11, 2022)

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❓ Faqs

• Are UMIs not actually unique? (November 17, 2021)
• Why do we only consider highly variable genes? (November 11, 2021)
• Can RNA-seq techniques be applied to scRNA-seq? (November 11, 2021)
• What exactly is a ‘Gene profile’? (November 11, 2021)
• Why do we do dimension reduction and then clustering? Why not just cluster on the actual data? (November 11, 2021)
• Why is amplification more of an issue in scRNA-seq than RNA-seq? (November 11, 2021)

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📚 Tutorials

• Filtrado, representación y exploración de secuenciación de ARN de células únicas (October 07, 2021)

🖼️ Slides

• Una introducción al análisis de datos scRNA-seq (October 19, 2021)
• Introducción al análisis de datos de scRNA-seq (October 19, 2021)

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📚 Tutorials

• Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin (August 31, 2021)

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📚 Tutorials

• Analysis of plant scRNA-Seq Data with Scanpy (April 08, 2021)
• Inferring single cell trajectories with Scanpy (Python) (April 07, 2021)

🛠️ Workflows

• scRNA Plant Analysis (April 08, 2021)

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📰 News

• New Tutorial: Downstream Single-cell RNA Plant analysis with ScanPy (March 30, 2021)

📚 Tutorials

• Filter, plot and explore single-cell RNA-seq data with Scanpy (March 24, 2021)
• Generating a single cell matrix using Alevin (March 03, 2021)

🛠️ Workflows

• CS3_Filter, Plot and Explore Single-cell RNA-seq Data (March 24, 2021)
• Combining datasets after pre-processing (March 03, 2021)
• Generating a single cell matrix using Alevin (March 03, 2021)

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🖼️ Slides

• An introduction to scRNA-seq data analysis (January 29, 2021)

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🖼️ Slides

• Dealing with Cross-Contamination in Fixed Barcode Protocols (March 17, 2020)

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🖼️ Slides

• Clustering 3K PBMCs with Scanpy (February 28, 2020)

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📚 Tutorials

• Clustering 3K PBMCs with Scanpy (December 19, 2019)

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📚 Tutorials

• Single-cell quality control with scater (October 23, 2019)

🛠️ Workflows

• Scater (October 23, 2019)

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📚 Tutorials

• Pre-processing of 10X Single-Cell RNA Datasets (September 11, 2019)

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📚 Tutorials

• Downstream Single-cell RNA analysis with RaceID (March 25, 2019)

🛠️ Workflows

• RaceID Workflow (March 25, 2019)

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📚 Tutorials

• Pre-processing of Single-Cell RNA Data (February 22, 2019)
• Understanding Barcodes (February 20, 2019)

🖼️ Slides

• Plates, Batches, and Barcodes (February 16, 2019)

🛠️ Workflows

• CelSeq2: Single Batch (mm10) (February 22, 2019)
• CelSeq2: Multi Batch (mm10) (February 22, 2019)

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