UCSC Track Hub links are available now for PhenoGen HRDPv6 data with more coming soon. Transcriptomes and Strain/Tissue specific read depth tracks are available. Go to Downloads -> UCSC Track Hubs. Coming soon: Sampled Read depth tracks and strain specific splice junctions

HRDPv6 based on the rn7.2 genome is available on the REST API and updated R function file as of 9/28/22. We have 58 HRDP strains and the transcriptome includes predicted alternative polyA sites. The downloads section also provides links to the datasets.

HRDP v6 and rn7 are now available on PhenoGen. HRDP v6 includes 58 strains. WGCNA and eQTLs for v6 are coming, but expression and the reconstructed transcriptome are available today.

Last week we released a quick REST update to populate dataset metadata at /downloads/dataset. The R file is also updated with new methods to get tables of samples/protocols/processing pipeline details for each dataset.

We now have an R file with methods to call the REST API. This will allow you to pull full datasets from PhenoGen into R directly! We'll expand it with the API, but for now get it from github.com/TabakoffLab/Pheno… and check back often as we continue to update.

Have you looked at the REST API documentation? We hope you find it helpful both in browsing available functions and providing complete details to call each function. Example calls can be generated for many different languages. rest-doc.phenogen.org/

We are also including new strains and moving small RNA-Seq data to rn7.2. For the new version we are predicting miRNAs from sequence data in 45 HRDP strains via multiple methods. This data is still running through the prediction steps. It's further out from release but is coming.

With the update to rn7.2 we are moving to HRDP v6. v6 is based on 58 strains of the HRDP including some FXLE/LEXF strains. Brain and liver include 58 strains. Kidney includes ~3 replicates for 28 HXB/BXH strains. Heart includes 1 rep of 20 HXB/BXH strains w/4 reps of BXLx/SHR.