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

• Epigenetics / Formation of the Super-Structures on the Inactive X
• Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 📝 ⚙️
• Single Cell / Analysis of plant scRNA-Seq Data with Scanpy
• Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
• Single Cell / Inferring single cell trajectories with Monocle3 (R) 📝
• Single Cell / Clustering 3K PBMCs with Scanpy
• Single Cell / Converting NCBI Data to the AnnData Format 📝 ⚙️
• Single Cell / Converting between common single cell data formats ⚙️
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets
• Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) 📝
• Single Cell / Generating a single cell matrix using Alevin and combining datasets (bash + R) 📝 ⚙️
• Single Cell / Inferring single cell trajectories with Scanpy 📝
• Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat 📝
• Transcriptomics / Reference-based RNA-Seq data analysis ✍️
• Transcriptomics / Small Non-coding RNA Clustering using BlockClust
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
• Transcriptomics / Genome-wide alternative splicing analysis 📝
• Transcriptomics / RNA-RNA interactome data analysis

Slides

• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana

Video Recordings

• Single Cell / Clustering 3K PBMCs with Scanpy 💬 🗣
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets 💬 🗣

Events

• Workshop on high-throughput sequencing data analysis with Galaxy 🧑‍🏫
• Workshop on high-throughput sequencing data analysis with Galaxy 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

30 Merged Pull Requests

See all of the github Pull Requests and github Commits by Pavankumar Videm.

• Scanpy 3k PBMCs tutorial update history and workflow links
  single-cell
• correct the scanpy tool names in the tutorial
  single-cell
• Update Single-cell PBMC 3k clustering tutorial
  single-cell
• SnapATAC2 tutorial: update data-library.yaml
  single-cell
• Typo DESeq2 hands.on in Ref-based tutorial
  transcriptomics

Reviewed 30 PRs

We love our community reviewing each other's work!

• Added MIGHTS tag
  single-cell
• Update ref based
  transcriptomics
• updated deseq2 paramter selection
  transcriptomics
• Update gta2024-single-cell.md
  template-and-tools
• Add a new question about gene annotations to PBMC3k tutorial
  template-and-tools
  single-cell

News

External Links

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