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Release note 11.27.23

5 months ago by Marko Marinkovic

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

Users who access CAVATICA 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 CAVATICA.

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.

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).