bioc2020anno's People
bioc2020anno's Issues
Question: how best to integrate gene annotation with tidybulk?
Hello,
There was a question at our workshop at Bioc2020 (tidytranscriptomics) about whether there was any intended complimentary use of tidybulk with the annotation resources described in the previous workshop
(your workshop).
I thought it was a good question and I've made a note here that we could maybe add some info on how to do that to future tidybulk workshops e.g. showing how to get and add gene symbols to a Drosophila RNA-seq counts table (tidybulk has an ensembl_to_symbol
function but it only works for human and mouse).
But was wondering if what I've put (below) is how you'd recommend doing this?
# install annotation packages for species
# BiocManager::install(c("Organism.dplyr", "TxDb.Dmelanogaster.UCSC.dm6.ensGene", "org.Dm.eg.db"))
# load library
library(Organism.dplyr)
# get annotation
src <- src_organism("TxDb.Dmelanogaster.UCSC.dm6.ensGene")
anno_table <- tbl(src, "id") %>%
# select desired columns
dplyr::select(ensembl, symbol) %>%
# keep one symbol per gene id
group_by(ensembl) %>%
filter(row_number()==1) %>%
# convert to tibble
collect()
# add symbols to counts table
counts_annot <- left_join(counts_tt, anno_table, by = c("feature" = "ensembl"))
Cheers,
Maria
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. ๐๐๐
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google โค๏ธ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.