OmicSoft Suite v12.5 is now available, with several new improvements for NGS analysis and exploration of curated omics data. Check out the full details in the OmicSoft Help menu’s “Change Log”.
With the new FASTQ download function, you can now simultaneously retrieve associated metadata from both the SRA and GEO repositories, ready to attach to your project files. The new module also supports previewing the data to ensure you chose the right project.
Figure 1. Preview both SRA and GEO metadata for your SRA downloads before downloading, to make sure that you are downloading the correct datasets.
Mass Spectrometry proteomics comparisons
The new Land database “ClinicalProteomicTumor” incorporates multi-omics cancer profiling studies from the CPTAC repository. These data focus on Mass Spectrometry (MS) data, but also includes RNA-seq, miRNA-seq, mutation, CNV, and methylation data.
In addition to sample-level protein expression data, you can explore statistical comparisons at the protein level, and compare differential expression patterns between protein and RNA between cohorts.
Figure 2. New MS comparisons allow deeper interrogation of proteomics datasets curated by the Omicsoft team, such as CD8+ inflamed (interferon-γ signaling) vs CD8− inflamed (platelet degranulation) tumors in clear cell Renal Cell Carcinoma (ccRCC) from PDC000127, at the RNA and protein level. (A) Differentially-regulated genes at the RNA level, calculated by DEseq2. (B) Differentially-regulated genes at the protein level, calculated by general linear model. Top up-regulated proteins were selected to illustrate concordance with RNA-level up-regulation. (C) Comparison of direction and magnitude between RNA (X-axis) and Protein (Y-axis) differential expression. Genes measured only at the RNA-level are plotted with a fold-change=0 on the Y-axis.
OmicSoft Studio installer supports improved options for updating to new versions of the software.
OmicSoft Lands API update
The latest update to OmicSoft Lands API (1.3) now supports REST interface to submit SQL queries. In addition, several improvements to query submission performance and bug fixes were addressed. Download the latest client and release notes details from my.qiagendigitalinsights.com.
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