Pavankumar Videm
Affiliations
Contributions
The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.
Editorial Roles
This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.
- Single Cell
- Applying single-cell RNA-seq analysis
- Introduction to Galaxy and Single Cell RNA Sequence analysis
- Applying single-cell RNA-seq analysis in Coding Environments
Tutorials
- Single Cell / Importing files from public atlases π§
- Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat π π§
- Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) π π§
- Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy π§
- Single Cell / Combining single cell datasets after pre-processing π§
- Single Cell / Analysis of plant scRNA-Seq Data with Scanpy βοΈ
- Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets βοΈ π§
- Single Cell / Inferring single cell trajectories with Monocle3 π§
- Single Cell / Downstream Single-cell RNA analysis with RaceID βοΈ
- Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 π βοΈ π§
- Single Cell / Inferring single cell trajectories with Scanpy (Python) π§
- Single Cell / Converting NCBI Data to the AnnData Format π βοΈ π§
- Single Cell / Generating a single cell matrix using Alevin π§
- Single Cell / Converting between common single cell data formats βοΈ π§
- Single Cell / Generating a single cell matrix using Alevin and combining datasets (bash + R) π βοΈ π§
- Single Cell / Inferring single cell trajectories with Scanpy π π§
- Single Cell / Clustering 3K PBMCs with Scanpy βοΈ π§
- Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution π§
- Single Cell / Pre-processing of 10X Single-Cell RNA Datasets βοΈ π§
- Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution π§
- Single Cell / Inferring single cell trajectories with Monocle3 (R) π π§
- Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) π§
- Epigenetics / Formation of the Super-Structures on the Inactive X βοΈ π§
- Proteomics / Metaproteomics tutorial π§
- Contributing to the Galaxy Training Material / Creating content in Markdown π§
- Transcriptomics / Genome-wide alternative splicing analysis π π§
- Transcriptomics / Reference-based RNA-Seq data analysis βοΈ π§
- Transcriptomics / Small Non-coding RNA Clustering using BlockClust βοΈ π§
- Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana βοΈ π§
- Transcriptomics / RNA-RNA interactome data analysis βοΈ
- Ecology / Production d'indicateurs champs de bloc π§
Slides
- Single Cell / Single-cell Formats and Resources π§
- Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana βοΈ π§
Video Recordings
- Single Cell / Clustering 3K PBMCs with Scanpy π¬ π£
- Single Cell / Pre-processing of 10X Single-Cell RNA Datasets π¬ π£
Events
- Workshop on high-throughput sequencing data analysis with Galaxy π§βπ«
- Workshop on high-throughput sequencing data analysis with Galaxy π§βπ«
- Galaxy Training Academy 2024 π§βπ«
GitHub Activity
github Issues Reported
33 Merged Pull Requests
See all of the github Pull Requests and github Commits by Pavankumar Videm.
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add WF tests for scrna basic pipeline
single-cell
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Add scrna-plant WF tests
single-cell
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add workflow test for single-cell raceid tutorial
single-cell
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Scanpy 3k PBMCs tutorial update history and workflow links
single-cell
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correct the scanpy tool names in the tutorial
single-cell
Reviewed 32 PRs
We love our community reviewing each other's work!
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SPOC CoFest blog post
news
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Update CoFest
template-and-tools
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Added MIGHTS tag
single-cell
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Update ref based
transcriptomics
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updated deseq2 paramter selection
transcriptomics
News
New Tutorials: Whole transcriptome analysis of Arabidopsis thaliana
10 April 2021
Plant lovers are in luck! A new tutorial on this fascinating kingdom has been added to the GTN. It details the necessary steps to identify potential targets of brassinosteroid-induced miRNAs. Brassinosteroids are phytohormones that have the ability to stimulate plant growth and confer resistance against abiotic and biotic stresses. These characteristics have led to great interest in the field of biotechnology due to its potential for increasing agricultural productivity.
Single cell subdomain re-launch: Unified and feedback-driven
12 October 2023
The European Galaxy Days 2023 CoFest combined the forces of administrator, developer and trainer to update and re-launch the single cell Galaxy instance. Where previously there were two subdomains each with their own sets of tools, there is now a unified subdomain with re-categorized tools that makes sense for users.
Galaxy Single-cell Community: Year in Review
22 December 2023
πEmbarking on a cosmic journey, the Galaxy Single-cell Community has clustered together to unveil a constellation of tools, making strides in RNA-stellar discoveries and creating out-of-this-world workflows. With a commitment to battling work duplication across the multiverse, this community is boldly charting a course for global domination, proving that when it comes to bioinformatics, the Galaxy is the limit!β¨