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License: CC BY
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nf-core/differentialabundance: v1.4.0 - 2023-11-27

Authors: WackerO; Jonathan Manning; Azedine Zoufir; nf-core bot; Alexander Peltzer; Cristina Tuñí i Domínguez; Dave Carlson; +4 Authors

nf-core/differentialabundance: v1.4.0 - 2023-11-27

Abstract

This PR contains a particularly important fix in https://github.com/nf-core/differentialabundance/pull/20, which resolves a long-standing issue in proper usage of abundance values from the rnaseq workflow. Users can now take the lengths from that workflow (using rnaseq >=v3.13.2) and pass them to this workflow to account for transcript length biases across samples. What's Changed Post 1.3.1 release changes by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/186 Fix sample metadata table in the html report not paginating by @davidecarlson in https://github.com/nf-core/differentialabundance/pull/195 Fix GSEA indent in report by @WackerO in https://github.com/nf-core/differentialabundance/pull/190 Add optional scree plot to report by @WackerO in https://github.com/nf-core/differentialabundance/pull/192 Enable all genes for exploratory by @WackerO in https://github.com/nf-core/differentialabundance/pull/188 Add DESeq text to report by @WackerO in https://github.com/nf-core/differentialabundance/pull/193 Added colors to volcano by @WackerO in https://github.com/nf-core/differentialabundance/pull/194 Document correct RNAseq matrix usage by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/200 Update DESeq2/Limma by @WackerO in https://github.com/nf-core/differentialabundance/pull/201 Add design to report by @WackerO in https://github.com/nf-core/differentialabundance/pull/189 Transcript lengths for DESeq2 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/203 Release v1.4.0 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/204 V1.4.0 fixes by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/206 Dev -> master for v1.4.0 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/205 New Contributors @davidecarlson made their first contribution in https://github.com/nf-core/differentialabundance/pull/195 Full Changelog: https://github.com/nf-core/differentialabundance/compare/1.3.1...1.4.0

  • BIP!
    Impact byBIP!
    citations
    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).
    3
    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.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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citations
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!
3
Top 10%
Average
Average