v114 released!

March 29, 2021 —

Announcing v114 release of the ENCODE portal, highlighted by the following updates: 

  • Added DOIs to Dataset pages
  • Added WalkMe link under “Help” menu in toolbar
  • Implemented RNAget search page
  • Modified and fixed bugs in Gene search
  • Fixed bug affecting batch downloading from Cart
  • Adjusted clickable mouse diagram image
  • Adjusted sorting of files displayed on Experiment pages
  • Fixed bug where File tables on Reference Filesets were missing Files
  • Fixed UI bug affecting Datasets where all visualizable files are deprecated
  • Created DM6, DM3, Ce10, Ce11, mm10 M21, GRCh38 V33 genome tracks for Valis genome browser
  • Allowed bed9 tracks to be collapsed on Valis genome browser
  • Fixed bug where Valis genome browser would display wrong reference genome tracks
  • Implemented default selection of “preferred default” for Cart genome browser
  • Allowed visualization of WGBS data generated using the GemBS pipeline
  • Prevented visualization of dense bigBeds generated using the GemBS pipeline
  • Added mapped_run_type information to File report columns and to File summary pages and modals
  • Added Element activity location and Organism facets to Transgenic enhancer experiment search page
  • Added new assay terms “GRO-cap”, “GRO-seq”, and “snRNA-seq”
  • Added new enum values “read annotations” and “sparse transcript count matrix” to File output_type, and “Parse Single Cell Whole Transcriptome Kit” to Library construction_method to support submission of SPLiT-seq data
  • Added “v33” and “M26” enums for File genome_annotation, and “GRCm39” for File assembly
  • Added “mAID” enum to Genetic Modification introduced_tags
  • Adjusted Library linkers property and added “Nucleobond PC Giga Kit” enum value to extraction_method
  • Added calculated “read_depth” property for STAR Quality Metrics
  • Added analysis_objects property to Annotations
  • Updated biosample summaries to include post_nucleic_acid_delivery_time and post_differentiation_time information
  • Updated calculation of CRISPR screen assay titles, introducing new “growth screen” assay titles
  • Added QC tables to DNase-seq Experiment Series pages
  • Added audit to flag inconsistent units used in Differentiation Series
  • Moved auditing of DNase-seq processed data from Experiments to Analyses
  • Fixed bug in WGBS audit
  • Embedded assay_title, annotation_type, target, and biosample_ontology in Files
  • Removed duplicated search boost value for Datasets

v114 software version: https://github.com/ENCODE-DCC/encoded/releases/tag/v114.0

All of the source code used for the portal website is open source and available through our repository hosted at GitHub (www.github.com/ENCODE-DCC/)