Subina Mehta
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.
- Topic: Proteomics
- Learning Pathway: Clinical metaproteomics workflows within Galaxy
- Learning Pathway: Neoantigen discovery using the iPepGen pipeline
- Learning Pathway: Proteogenomics
Tutorials
- Proteomics / metaQuantome 1: Data creation ✍️ 🧐
- Proteomics / Proteogenomics 2: Database Search ✍️ 🧐
- Proteomics / Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides ✍️ 🧐
- Proteomics / Peptide Library Data Analysis 🧐
- Proteomics / Clinical Metaproteomics 4: Quantitation ✍️ 🧐
- Proteomics / Machine Learning Modeling of Anticancer Peptides 🧐
- Proteomics / Neoantigen 1a: Fusion-Database-Generation ✍️ 🧐
- Proteomics / EncyclopeDIA ✍️ 🧐
- Proteomics / metaQuantome 3: Taxonomy ✍️ 🧐
- Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker 🧐
- Proteomics / Clinical Metaproteomics 3: Verification ✍️ 🧐
- Proteomics / Clinical Metaproteomics 2: Discovery ✍️ 🧐
- Proteomics / Neoantigen 4: Variant Annotation ✍️ 🧐
- Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method 🧐
- Proteomics / Statistical analysis of DIA data 🧐
- Proteomics / Library Generation for DIA Analysis 🧐
- Proteomics / Proteogenomics 3: Novel peptide analysis ✍️ 🧐
- Proteomics / Label-free data analysis using MaxQuant 🧐
- Proteomics / Clinical Metaproteomics 5: Data Interpretation ✍️ 🧐
- Proteomics / DIA Analysis using OpenSwathWorkflow 🧐
- Proteomics / metaQuantome 2: Function ✍️ 🧐
- Proteomics / Metaproteomics tutorial ✍️ 🧐
- Proteomics / Neoantigen 5a: Predicting HLA Binding ✍️ 🧐
- Proteomics / Proteogenomics 1: Database Creation ✍️ 🧐
- Proteomics / Neoantigen 3: PepQuery2 Verification ✍️ 🧐
- Proteomics / Neoantigen 1b: Non-Reference-Database-Generation ✍️ 🧐
- Proteomics / Neoantigen 2: Database merge and FragPipe discovery ✍️ 🧐
- Proteomics / Clinical Metaproteomics 1: Database-Generation ✍️ 🧐
- Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data ✍️
- Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) ✍️
Slides
- Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling 🧐
- Microbiome / Introduction to metatranscriptomics ✍️ 🧐
FAQs
- Is it possible to replace the existing alignment tools such as HISAT and Freebayes with other tools?
- Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference?
- Why do we use FASTQ interlacer and not the FASTQ joiner?
- Can we use the ASaiM-MT workflow on multiple input files at the same time?
- In the MVP platform, is it possible to view the genomic location of all the peptides?
- Example histories for the proteogenomics tutorials
- Can I use these workflows on datasets generated from our laboratory?
- The workflows contain several Query tabular for text manipulation, is there a tutorial for that?
- What kind of variants are seen in the output?
- How many search engines can you use in SearchGUI?
- Can this ASaiM workflow be used for single-end data?
- Why do we have a variant mapping file when it is not being used in the workflow?
- Why don't we perform the V-Search dereplication step of ASaiM for metatrascriptomic data?
Video Recordings
- Proteomics / Proteogenomics 3: Novel peptide analysis 💬 🗣
- Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data 🗣
- Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) 🗣
Events
GitHub Activity
github Issues Reported
47 Merged Pull Requests
See all of the github Pull Requests and github Commits by Subina Mehta.
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Update neoantigen.md
template-and-tools -
Update neoantigen.md
template-and-tools -
added neoantigen to learning pathways
template-and-tools -
edited the typo
proteomics -
Update Clinical metaproteomics tutorials
proteomics
Reviewed 31 PRs
We love our community reviewing each other's work!
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Editing names in proteomics folder
template-and-toolsproteomics -
Editing numbers in neoantigen tutorials
proteomics -
Update tutorial.md
proteomics -
Update tutorial.md
proteomics -
Update tutorial.md
proteomics
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