Welcome to the GitHub organisation from the Umeå Plant Science Centre Bioinformatics Facility (UPSCb in short).
| Repository | Description | DOI |
|---|---|---|
| course-web | A repository to generate a simple website in nodejs to serve workshop content |  |
| Dockerfile | A collection of Dockerfile to create a variety of containers for bioinformatics analyses and workshops |  |
| project-template | A template to setup projects, based on the UPSCb guidelines for reproducibility | not relevant |
| SeidRFile | A repository containing an R package to interact with file in the seidr format (sf) generated by sei∂r |  |
| UPSCb-common | Common scripts and templates from the UPSCb. Cite it if you use it in your research. |  |
If possible, please cite the tutorials if you (re-)use them for your teaching. Mind the license and get in touch if you use these commercially.
| Repository | Description | DOI |
|---|---|---|
| Tutorial_template | A template to create learnR tutorials | not-relevant |
| Tutorial_01_data_science_intro |  |
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| Tutorial_02_exploratory_data_analysis |  |
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| Tutorial_03_differential_gene_expression |  |
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| Tutorial_04_gene_set_enrichment_analysis |  |
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| Tutorial_05_ensemble_gene_set_enrichment_analysis |  |
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| Tutorial_06_differential_transcript_usage |  |
| Repository | Description | Manuscript | DOI |
|---|---|---|---|
| aba | Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication |  |
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| arabidopsis-floral-induction | Characterisation of metabolic changes associated with floral transition in Arabidopsis: variations in raffinose synthesis contribute to the determination of flowering time. |  |
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| NorWood |  |
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| spruce-seasonal-needles |  |
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| UPSCb | The original repository of the UPSC Bioinformatics Facility, holds multiple published projects, their analyses and links to their datasets | TBA |  |
| Repository | Description | DOI |
|---|---|---|
| RnaSeqTutorial | A long lived repository from an R package that was used for RNA-Seq workshops. |  |
| Repository | Description |
|---|---|
| MARVEL | A fork of the MARVEL repository used during the initial phase of the spruce v2.0 genome sequencing project |