annotables

annotables copied to clipboard

Can you make tables with ensembl versions (on genes & transcripts)?

msierk

annotables installation

2

hi~ I used the R (3.5.0) to install annotables packages. But I got some Errors. Commands: >install.packages("devtools") devtools::install_github("stephenturner/annotables") Errors: > devtools::install_github("stephenturner/annotables") Error in curl::new_handle() : An unknown option was passed...

AIBio

Hi, I find your package very useful, but I'm not very R savvy. Is it possible to add new organisms to annotables? I'm interested in Mmul10 (Macaca mulatta). Thanks for...

mmorselli17

Update Question

3

If I want to update annotables for a build more recent than your git hub, is it simply a matter of cloning and building the annotables package? In other words,...

thompj27

update readme

1

need to update documentation with changes made in #6 by @aaronwolen to document automated creation of new datasets based on YAML files

stephenturner

better version/build management

3

with the changes in #6 it's much easier to recreate annotation tables. the files are named e.g. `galgal5`, but which version/build is actually used depends on what's current in ensembl....

stephenturner

do something with MSigDB

1

See http://bioinf.wehi.edu.au/software/MSigDB/ This could be useful in all sorts of ways.

stephenturner

Zebrafish annotation

1

Could you please add Zebrafish to the list? @demis001

demis001

Grcm38 gene annotations are Grcm39 based!

1

I loaded annotables (version 0.2.0) in R and found the coordinates of ensemble annotated genes in grcm38 are acutally the coordinates of ensemble annotated genes based on the updated genome...

userBi0