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TranscriptPeak
Transcript-coordinate meRIP/m6A-seq and RIP-seq peak calling with browser visualization, gene mapping, transcript-region annotation and Linux CLI automation.
v1.11.2Web-version + Linux CLI-version
Open TranscriptPeak SciBerg Software
Bioinformatics applications built for reproducible sequencing workflows.
Download the latest SciBerg releases for RNA enrichment peak calling, transcript quantification, expression-matrix analysis and short-read alignment. Browser applications run locally from standalone SciBerg-branded HTML packages; Linux releases support reproducible workstation and pipeline workflows. SciBerg software is free for non-commercial research and education; commercial use requires a separate written SciBerg license.
Applications
Five focused tools across the RNA-seq workflow.
Each application has its own release page, downloads and comprehensive user guide.
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GenomePeak
Genome-coordinate RNA enrichment peak calling with optional GTF/GFF3 annotation or annotation-free whole-genome scanning.
v1.1Web-version + Linux CLI-version
Open GenomePeakQ
RNAQuant
Transcript-level fragment quantification from transcriptome- or genome-aligned BAM files with EM handling of multimappers and combined raw/estimated/TPM matrices.
v0.1.4Web-version + Linux CLI-version
Open RNAQuantM
RNA Matrix Studio
Count-matrix consolidation, TMM-style normalization, correlation, PCA, batch-aware exploration and edgeR/limma-aligned DGE workflows.
v2.0Web-version + Linux CLI-version
Open RNA Matrix StudioS
SciAlign
Portable static Linux x86-64 ungapped short-read aligner with FM-style indexing, whole-read/seed mismatch modes and multithreaded index construction.
v0.2.2Linux only
Open SciAlign Workflow map
From alignment to statistical analysis.
The applications are independent and can be combined where appropriate.
| Application | Primary input | Primary output | Interfaces |
|---|---|---|---|
| SciAlign | FASTA + FASTQ | SAM + mapping statistics | Linux |
| RNAQuant | BAM + reference | Transcript count / TPM matrices | Web-version + Linux CLI-version |
| RNA Matrix Studio | Raw count tables | Consolidated matrices, PCA, DGE | Web-version + Linux CLI-version |
| TranscriptPeak | Transcriptome BAM + FASTA | Transcript-coordinate peaks | Web-version + Linux CLI-version |
| GenomePeak | Genome BAM (+ optional GTF/GFF3) | Genome-coordinate peaks | Web-version + Linux CLI-version |
Legal & licensing
Free for non-commercial research. Commercial use requires a SciBerg license.
The following summary applies to SciBerg-owned portions of the distributed software. Third-party components remain subject to their own license terms. The complete legal notice supplied with every release controls where this summary is abbreviated.
Non-commercial research use
SciBerg software may be installed, copied internally and used free of charge for non-commercial scientific research, teaching, academic training and academic evaluation. Copyright, attribution and legal notices must be preserved.
Commercial license required
A separate written license from SciBerg e.Kfm is required before any commercial, revenue-generating or for-profit use, including internal commercial R&D, contract research, consulting, fee-for-service analysis, paid SaaS/hosted analysis, product development, customer deliverables or other use supporting a commercial product or service.
Redistribution and hosting
Without written permission, no right is granted to sell, rent, lease, sublicense, commercially redistribute, commercially host or bundle the software as part of a paid service. SciBerg names, logos and branding must not be used to imply endorsement, certification or partnership without authorization.
Research-use software
The applications are research and analytical-development software. They are not medical devices and are not validated for clinical diagnosis, patient management, treatment selection or other regulated clinical decisions. Scientific outputs require independent review and appropriate validation.
User data and responsibility
SciBerg claims no ownership of user input data or analysis outputs merely because they are processed by the software. Users remain responsible for data rights, confidentiality, applicable institutional/ethical/legal requirements and evaluation of the scientific validity of generated results.
Warranty, liability and third parties
The software is supplied “AS IS” and “AS AVAILABLE”, without warranties of accuracy, fitness, merchantability or error-free operation, to the extent permitted by law. Third-party software and libraries retain their own copyright and license terms.
Commercial licensing and complete terms. Commercial use requires a separate written SciBerg agreement before use. Contact SciBerg for commercial licensing or read/download the complete SciBerg Research Use License and Legal Notice. By downloading, copying, installing or using the software, the user accepts the supplied terms unless a separate written agreement with SciBerg e.Kfm applies.