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epi2me-labs/wf-transcriptomes: v2.0.1

Authors: Neil Horner; Sarah Griffiths; Chris Wright; Sam Nicholls; Natalia Garcia Garcia; Kiah McIntosh; Matthew Parker; +5 Authors

epi2me-labs/wf-transcriptomes: v2.0.1

Abstract

This patch release of wf-transcriptomes handles an additional quantification failure edge case that was not observed before release, fixes issues encountered by users during joint discovery when providing many samples, and makes some improvements to the volcano plot in the output report. Users of wf-transcriptomes v2.0.0 who have encountered issues during discovery and quantification should adopt this release. Fixed "Error in full_join" encountered during runPerSampleBambuQuant when all read classes have no compatible transcript assignment. An empty quant table is correctly emitted instead. "unable to find an inherited method for function 'rowData'" encountered during runJointBambuDiscover when providing many samples. The workflow now correctly handles data spilled to disk by bambu discover. Fatal memory error (exit 137) encountered during collateBambuQuant when providing many samples with a large reference. Collation now uses a two-pass approach to process the per-chunk RDS results to avoid exhausting memory limits. Volcano plot class counts incorrect when log2FoldChange or padj columns contained NA values. IGV track not correctly loading in EPI2ME Desktop when a sample consists of a single input BAM. Added Volcano plots now display the full y-axis range and include a slider to control the y-axis range maximum, which can be useful to exclude low p-value outliers. Changed Adjusted p-values below 0.001 in the volcano selection table were rounded to 0.000, these are now shown in scientific notation.

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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Average
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Average