Release notes

Azure now available on the CGC

To help you reduce costs and run analyses more effectively and efficiently in compute locations that are closer to your data, we have introduced a new Azure region on Cancer Genomics Cloud (CGC). The Azure South Central US region can now be selected as the project location when creating a new project on the CGC, meaning that data in such projects will be stored and processed using Azure cloud capacities. On top of that, we have also added support for attaching Azure storage buckets as volumes.

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

Users who access the CGC 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 CGC.

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).