Release note

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Release note

Single and Global logout flows defined by SAML protocol are now available for SSO  

Users who access the Seven Bridges Platform through Single Sign-On (SSO) can now perform Single (IdP Initiated) logout to log out of multiple SSO sessions, in a single click. Also, it is now possible to initiate Global (SP initiated) logout flow from the Seven Bridges Platform.

Recently published apps  

We have published the following tools in our Public Apps gallery:  

  • Tximport, a tool that imports and summarizes transcript-level estimates for transcript and gene-level analysis based on the tximport R/Bioconductor package. It is designed to simplify the import of transcript-level abundances, estimated counts, and effective lengths from a variety of upstream tools, for downstream transcript-level or gene-level analysis.  

Three tools from the SplAdder (3.0.4) toolkit:  

  • SplAdder build constructs splicing graphs and extracts alternative splicing events.  
  • SplAdder test differentially tests the usage of alternative event between two groups of samples.  
  • SplAdder viz generates visual overviews of splicing graphs and alternative events. SplAdder viz uses results generated by SplAdder build or SplAdder test to create plots.  

Five tools from the Qualimap 2.3 toolkit:  

  • Qualimap Multi-sample BAM QC reports QC metrics computed in BAM QC analysis combined for multiple samples.  
  • Qualimap Compute counts calculates how many reads are mapped to each region of interest.  
  • Qualimap RNA-seq QC reports quality control metrics and bias estimations for whole transcriptome sequencing.  
  • Qualimap Counts QC analyzes count data to assess a differential expression between two or more conditions.  
  • Qualimap BAM QC reports information for the evaluation of the quality of the provided alignment data.  

Six tools from the RSeQC 5.0.1 toolkit:  

  • RSeQC read distribution calculates how mapped reads were distributed over genomic features.  
  • RSeQC junction annotation compares detected splice junctions to the reference gene model.  
  • RSeQC inner distance is used to calculate the inner distance (or insert size) between two paired RNA reads.  
  • RSeQC infer experiment is designed to estimate how RNA-seq data is configured.  
  • RSeQC read duplication calculates read duplication rate determined by mapping position or sequence of the read.  
  • RSeQC bam stat summarizes mapping statistics of the provided alignment file.  

The Tidyproteomics 1.5.2 toolkit:  

  • Expression analysis – used for proteomics differential expression analysis.  
  • Data input and summary – used for loading protein or peptide data.  
  • Data subsetting and summary – used for subsetting protein or peptide data.  
  • Abundance normalization – used for abundance normalization of the protein or peptide data.  
  • Enrichment analysis – used for enrichment analysis after differential expression analysis.  
  • Annotate data – used for proteomics data annotation before enrichment analysis.  

Improved storage cost breakdown  

To meet the need for precise allocation of storage costs within a division, we have implemented a solution that enables precise per-project storage breakdown on the Seven Bridges Platform.  

The new solution includes improved accuracy in per-project storage breakdown, facilitating precise cost allocation, as well as elimination of storage size discrepancies between per-project and per-division calculations. This presents a great benefit both for users with administrative roles in divisions and Platform users in general as it increases transparency and provides a better insight into storage cost distribution.  

Recently updated apps  

TopHat2, a tool that aligns RNA-Seq reads to a genome to identify exon-exon splice junctions, just got updated to version 2.2.1 and upgraded to CWL version 1.2 (was previously available in CWL draft-2).