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debugs
add normalization option
add clustering option
remove aggregate and relative options

commit 320ecbdbb66701084c2b874c253945615a05c3e5
Author: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date:   Tue Jun 14 18:17:22 2022 +0200

    add argument maxEE

commit 2f734195aa134d40061f47ccb35faef3a9b44b08
Merge: b3c4f6d fc75a3e2
Author: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date:   Mon Jun 13 13:46:48 2022 +0200

    Merge branch 'master' into 2205_dev

commit b3c4f6df47fee5b38933c8746a3bd7fd7379684a
Author: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date:   Mon Jun 13 13:45:53 2022 +0200

    fix res aov alpha + updatemetadata

commit 99367be4
Author: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date:   Wed Jun 1 17:22:31 2022 +0200

    fixes

dada2_fun changes

See merge request !4

dada2: add cutadapt to trim primers for all type of data
fixes

when some samples don't pass filters

asvenn no need to specify levels when <= 7
dada fix single end mode orient sequences / search primers on reverse complement
dada fix output name of filterandtrim step
beta fix interpretation of factor to test

doing multiple plot.

add extension argument to inform R1 R2 pattern for paired data
change amplicon argument to "cutadapt". set to TRUE and inform sequence primers to trim primers with cutadapt.
add cutadapt step in singleend SOP (illumina/torrent).

fix message at ranomaly startup
add message when no significant features in aggregate

update

See merge request !3

bars: allow to keep sample order given by metadata
alpha: suppress fdr for pairwise wilcox and legend display
beta: plotly output

add secondary plot when cov argument is used

stats was done on raw table inducing NAs.

replace Fact argument by sample_labels boolean, allow user to display sample ids rather than group they belong for non splitted plot.
autoorder argument to apply or not automatic ordering of groups.