David Winter

Preferred citation?

3

Hi, Apologies if I've missed it somewhere in the docs, but is there a preferred way to cite the funannotate pipeline? We can cite the repository and version used, but...

Query building in R

10

(tagging @Monty9 and @htc502 on this as they've each brought i up recently) The query syntax used in esearch (and wrapped in `entrez_search`) is very powerful, but somewhat difficult to...

### Description of feature Many thanks to the developers of this workflow -- it's great to have a reproducible tool to automate the bulk of our amplicon sequencing. We are...

Following on from point (1) in #27 (which includes code for the answer even)

.paf to circos?

1

@KelliSmith17 is hell-bent on making circos plots, and has some code to convert the pafr table to the `karyotype` and `links` files required for this. If we can package it...

a function to covert paf formatted files to SYRI format would be v. helpful https://schneebergerlab.github.io/syri/fileformat.html

eg, report total coverage of a query/chromosome by all TEs, each class etc. Can likely re-use some of @KelliSmith17 summary/aggregation code here

Sure would be nice

New maintainer(s)

4

As is evident from the stack of open issues, I no longer have the capacity to maintain `rentrez` actively. In addition to not keeping pace with changes at NCBI and...