Standard consolidation
Combine one raw count file per sample into aligned matrices with missing targets filled as zero.
RNA Matrix Studio v2.0
From raw count files to QC, PCA and DGE.
RNA Matrix Studio consolidates raw count tables into multi-sample matrices, supports standard and automatic multi-biotype workflows, performs TMM-style normalization, correlation and PCA, and provides an edgeR/limma-aligned browser DGE workflow with exportable R code.
What it does
RNA Matrix Studio workflow.
Purpose-built scientific software with downloadable documentation and reproducible local workflows.
Multi-biotype mode
Automatically group recognized SEQIRA/eXpress-derived biotype files into one ordered sample matrix.
Normalization and batch
Choose TMM-style or library-size normalization and optionally inspect one-way batch-adjusted CPM/logCPM.
Correlation and PCA
Pearson/Spearman QC matrices and PCA with group coloring, labels, hulls and downloadable coordinates.
DGE exploration
Group contrasts, CPM filtering, batch covariates, moderated limma-style statistics and volcano plots.
Exact R workflow export
Download an edgeR/limma R script corresponding to the selected design for package-based final analysis.
Usage
Browser workflow.
The v2.0 application is browser-based. Required table columns are target_id, length and tot_counts:
1. Open RNA_Matrix_Studio_v2.0.html 2. Load count files and choose Standard or Multi-biotype mode 3. Assign sample group / replicate / batch metadata 4. Build raw matrix and select normalization 5. Review correlation and PCA 6. Configure group contrast and DGE 7. Download matrices, plots, DGE table and R script
Install / launch
Start the release locally.
tar -xzf RNA_Matrix_Studio_v2.0_linux.tar.gz cd RNA_Matrix_Studio_v2.0_linux chmod +x rna-matrix-studio ./rna-matrix-studio # The launcher opens the bundled HTML app in the system browser.
Research-use software. The Linux CLI-version download currently uses a desktop launcher for the same v2.0 browser application; it is not a separate native statistical engine. Use the exported edgeR/limma R script for package-identical publication workflows.