Bela

Demultiplexing with seperate index file

6

Hi! Raw Illumina reads sometimes come with the Index read as a separate file, so you get three files like that: S0_L001_I1_001.fastq.gz S0_L001_R1_001.fastq.gz S0_L001_R2_001.fastq.gz Where S0_L001_I1_001.fastq.gz contains the barcodes/indices. Is...

Hi! Thanks for this package! Very useful! We generate XLSX files for our users, where it would be useful to be able to activate the Data validation features of Excel...

Hi! I was getting the error `'arg' should be one of “lingoes”, “cailliez”` when using the demo data set or my own data. Use lingoes/cailliez instead of T/F fixed it...

ggvis doesn’t work together with shiny::validate

6

Hi! let me start by saying: ggvis is coming along nicely! Awesome! I was generating data.frames on the fly based on a dynaimc UI and ran into problems combining this...

taxonomy ranks are too restictive

26

Hi, in case one's taxonomy ranks fall outside of what is hard-coded in `mia::TAXONOMY_RANKS`, it breaks functions like `taxonomyRanks`. For example: ``` > agglomerateByRank(my_tse, "Strain") Error: 'rank' must be a...

Ribosomal RNA operon copy number correction / rrnDB support

2

Hi, maybe it would be interesting/useful to add support for things like the [rrnDB](https://rrndb.umms.med.umich.edu/). This is often combined with using absolute abundance measures (see #4) to get estimated genome copy...

Implementing dada-class and derep-class vectors

3

Hi! I am confused as to why many of the dada2 functions unlist their return value, if there is only one input/output object, e.g.: * https://github.com/benjjneb/dada2/blob/963f4e023023bc528177a2c04ab7f1ae5332461c/R/dada.R#L478 * https://github.com/benjjneb/dada2/blob/963f4e023023bc528177a2c04ab7f1ae5332461c/R/sequenceIO.R#L114 * https://github.com/benjjneb/dada2/blob/963f4e023023bc528177a2c04ab7f1ae5332461c/R/paired.R#L199...

DADA2-formatted reference database for SILVA 138.2

5

Hi, [SILVA 138.2](https://www.arb-silva.de/news/view/2024/07/11/silva-release-1382/) is out. Will there be an updated [DADA2-formatted reference database](https://benjjneb.github.io/dada2/training.html) made for it? It would be greatly appreciated. Thank you! Bela

Hi, [right now](https://github.com/r-lib/roxygen2/blob/b94b42ff7075da99e1324c058fe01c94ea9f6260/R/object-defaults.R#L43), only `logo.png` is used for package documentation. This could be amend, so also `logo.svg` will also be used. This would then bring it in line with https://pkgdown.r-lib.org/reference/build_favicons.html...