ranomaly merge requests
https://forgemia.inra.fr/umrf/ranomaly/-/merge_requests
2024-01-22T15:11:18+01:00
https://forgemia.inra.fr/umrf/ranomaly/-/merge_requests/7
Dev tax
2024-01-22T15:11:18+01:00
Etienne Rifa
Dev tax
Changes in Taxonomy assignation functions:
- include taxonomy ranks and prefix which was hardcoded (default is 7 ranks kingdom to species), this allow users to use databases with specific taxonomic rank numbers.
- previous change invol...
Changes in Taxonomy assignation functions:
- include taxonomy ranks and prefix which was hardcoded (default is 7 ranks kingdom to species), this allow users to use databases with specific taxonomic rank numbers.
- previous change involves adjustments in subsequent functions
Diff analysis:
- Use of `try()` on `DESeq2::DESeq` to prevent failure on specific comparison
https://forgemia.inra.fr/umrf/ranomaly/-/merge_requests/6
a function to create a heatmap from deseq2 output
2024-01-10T16:43:32+01:00
Philippe Ruiz
philippe.ruiz@inrae.fr
a function to create a heatmap from deseq2 output
a function to create a heatmap from deseq2 output
a function to create a heatmap from deseq2 output
https://forgemia.inra.fr/umrf/ranomaly/-/merge_requests/5
plsda update to integrate multilevel analyses and add some output
2024-01-10T10:55:23+01:00
Philippe Ruiz
philippe.ruiz@inrae.fr
plsda update to integrate multilevel analyses and add some output
I propose to integarte the multilevel approach in the `plsda_fun`.
The function use the `withinVariation` function of mixOmics for repeated measurments.
Their is also some supplémentary ouput.
It's works but maybe it's better to integra...
I propose to integarte the multilevel approach in the `plsda_fun`.
The function use the `withinVariation` function of mixOmics for repeated measurments.
Their is also some supplémentary ouput.
It's works but maybe it's better to integrate it in a dev branch
https://forgemia.inra.fr/umrf/ranomaly/-/merge_requests/4
dada2_fun changes
2022-04-04T16:01:34+02:00
Etienne Rifa
dada2_fun changes
+ 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).
+ add extension argument to inform R1 R2 pattern for paired data
+ f...
+ 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).
+ add extension argument to inform R1 R2 pattern for paired data
+ fixes
+ update wiki and usecase
https://forgemia.inra.fr/umrf/ranomaly/-/wikis/home#dada2-usage-according-to-raw-data-type
https://forgemia.inra.fr/umrf/ranomaly/-/merge_requests/3
update
2021-10-15T17:51:30+02:00
Etienne Rifa
update
lot of changes!!!
lot of changes!!!
Etienne Rifa
Etienne Rifa
https://forgemia.inra.fr/umrf/ranomaly/-/merge_requests/2
fix redundant codes
2021-06-08T18:18:44+02:00
Etienne Rifa
fix redundant codes
allowing the use of more than 2 reference databases
integrate idtaxa_assign_fasta_fun into assign_taxo,same process
allowing the use of more than 2 reference databases
integrate idtaxa_assign_fasta_fun into assign_taxo,same process
Etienne Rifa
Etienne Rifa
https://forgemia.inra.fr/umrf/ranomaly/-/merge_requests/1
add an argument to bars_fun to split graph as facet_wrap
2021-02-10T10:50:45+01:00
Philippe Ruiz
philippe.ruiz@inrae.fr
add an argument to bars_fun to split graph as facet_wrap
a new argument in `bars_fun()` named `split` to separate compositional barplot like `facet_wrap`
a new argument in `bars_fun()` named `split` to separate compositional barplot like `facet_wrap`