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Implementation of IsoformSwitchAnalyzeR #142
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Patch v1.0.1
Release of patch fix v1.0.2
Patch fix v1.0.3
Fix incorrect assignment of cluster groups
Hi Jesse, Thank you so much for submitting a pull request for IsoformSwitchAnalyzerR! I’ve added myself along with two other maintainers to help review it. @bensouthgate, if you’ve got a moment, could you take a look? Thanks again for your contribution! Best regards, |
@lathikaa Can you also replicate the changes to the metro-map which Jesse has committed using the original Canva template? |
Description of changes
In reference to issue #148
Dear rnasplice team, as my colleague discussed with you on slack on 15 February, I have added IsoformSwitchAnalyseR to the pipeline.
IsoformSwitchAnalyzeR is a powerful tool for identifying isoform switches in transcript data.
IsoformSwitchAnalyzeR takes a Salmon results directory as input. If it finds genes with isoform switches, it produces publication-quality plots visualising these switches. A separate set of switch plots is generated for each contrast if that contrast contains significant switches. Two .csv files are also created, a summary and the main data frame. The .rds of the main R-list is also returned.
This results in the following file structure:
isoformswitchanalyzer
|-- results
| |-- Condition1_vs_Condition2
| | |-- 01_switch_plot_gene1.pdf
| | |-- 02_switch_plot_gene2.pdf
| | |-- 03_switch_plot_gene3.pdf
| |
| |-- Condition2_vs_Condition3
| | |-- 01_switch_plot_gene4.pdf
| | |-- 02_switch_plot_gene5.pdf
| | |-- 03_switch_plot_gene6.pdf
|
|-- isoformswitchanalyzer_isoformfeatures.csv
|
|-- isoformswitchanalyzer_summary.csv
|
|-- switchlist.rds
Details
A new local module was added calling an R script in bin.
The module is called from the rnasplice workflow.
A new test for IsoformSwitchAnalyzeR was added.
Documentation, config scripts, etc. were updated according to the guidelines.
Some of the commits are from merges with the updated master branch.
The lint checks failed. But they also failed before I implemented the changes.
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).