https://github.com/bleekerlab/shiny_rnaseq_app
An Shiny application to explore RNA-seq results produced from the laboratory on tomato. Web application is private under password protection (please request access).
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.4%) to scientific vocabulary
Keywords
Repository
An Shiny application to explore RNA-seq results produced from the laboratory on tomato. Web application is private under password protection (please request access).
Basic Info
- Host: GitHub
- Owner: BleekerLab
- License: apache-2.0
- Language: R
- Default Branch: master
- Homepage: https://amsterdamstudygroup.shinyapps.io/tomato_gene_explorer/
- Size: 1.3 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Tomato gene explorer
A Shiny application to explore RNA-seq results from processed (= gene counts) data coming from mRNA-seq data.
Data provenance (ITAG2.4)
Genome references
Genomic references can be found on Zenodo Link.
Genome assembly and annotation ITAG2.4 were used:
- Genome FASTA: Slycopersicumchromosomes.2.50.fa.gz
- Genome annotation: ITAG2.4genemodels.gtf
Snakemake pipeline
To get the scaled gene counts, the v0.3.8 release of the snakemake_rnaseq pipeline was used:
- Link GitHub
- Link Zenodo
Dataset 01: 20 cultivated and wild tomato accessions
mRNA-seq files (5 parts):
- Part 1
- Part 2
- Part 3
- Part 4
- Part 5
Dataset 02: cultivated and wild tomato tissues
mRNA-seq files: Zenodo link
Samples S31 to S48 were used.
Dataset 03: S. lyc Elite x S. hab PI127826 F2 lines
mRNA-seq files (two parts):
- Parents and F1 (2017): Zenodo link
- F2 (2019): Zenodo link
Dataset 04: MYC1 knock-out and knock-down mutants
mRNA-seq files Zenodo link
Owner
- Name: Petra Bleeker laboratory
- Login: BleekerLab
- Kind: organization
- Email: P.M.Bleeker@uva.nl
- Location: University of Amsterdam
- Repositories: 6
- Profile: https://github.com/BleekerLab
Laboratory of Petra Bleeker at University of Amsterdam