Release note 11.27.23
about 1 year 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).