Excelra vs Pepkio: Bioinformatics Service Comparison

Quick Comparison Table

What Excelra Does

Excelra is a dry-lab computational biology contract research organization that processes omics datasets without running a wet lab. Research teams provide raw sequencing files (FASTQ), alignments (BAM), variant files (VCF), expression matrices, microarray data, mass spectrometry proteomics or metabolomics files, or Olink quantification tables.

Their analysis portfolio spans bulk RNA-seq, single-cell RNA-seq (clustering, cell-type annotation, trajectory analysis), spatial transcriptomics, whole genome and whole exome variant calling, epigenomics (ChIP-seq, ATAC-seq, DNA methylation), mass spectrometry proteomics, metabolomics, lipidomics, and multi-omics integration. Beyond standard omics workflows, Excelra offers computational drug discovery, target identification and validation, mechanism of action (MoA) modeling, structure-activity relationship (SAR) modeling, neoantigen identification, and HLA typing. They also maintain proprietary curated datasets, including the GOSTAR medicinal chemistry database and GOBIOM biomarker database.

Workflows use open-source tools such as FastQC, STAR, Bowtie, BWA, DESeq2, edgeR, limma, CellRanger, Seurat, Scanpy, GATK, and MACS2, along with graph neural networks and deep learning models. Deliverables include access to results through their cloud-based OP² (Online Pipeline Platform) portal with interactive plots and searchable tables, static PDF/HTML summary reports, normalized data matrices, and scientific consultation meetings. Enterprise biopharma teams engage Excelra for large-scale data biocuration, drug discovery pipelines, or dedicated FTE computational support.

What Pepkio Does

Pepkio provides dry-lab bioinformatics analysis for research teams with raw sequencing or omics datasets. Modalities cover bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics (10x Visium/Visium HD), WGS/WES variant calling, ChIP-seq, ATAC-seq, metagenomics, and proteomics.

Pipelines use open-source tools such as STAR, fastp, DESeq2, Seurat, and GATK. Pepkio delivers raw executable R and Python scripts, detailed parameter logs, normalized count matrices, differential analysis tables, editable vector figures (SVG, PDF), and a draft Methods section. Workflows can optionally be packaged as Nextflow or Snakemake pipelines in Docker or Conda environments.

Researchers communicate with the computational biologist assigned to their study. That access covers initial scoping, parameter adjustment during processing, and post-delivery support to rerun scripts or address reviewer comments.

Pepkio vs Excelra: Head-to-Head Comparison

How Do Analysis Scope and Organism Support Compare?

Pepkio focuses on core NGS and omics modalities, while Excelra also covers computational drug discovery and specialized mass spectrometry assays. Pepkio handles bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics, WGS/WES variant calling, ChIP-seq, ATAC-seq, metagenomics, and proteomics. Excelra supports these core NGS pipelines and also offers LC-MS/MS proteomics, metabolomics, lipidomics, glycoproteomics, SAR modeling, target validation, MoA elucidation, and HLA typing.

Both providers analyze data across human, mouse, rat, non-human primates, cell lines, microbial genomes, and major plant or animal model organisms. Accepted sample types include fresh frozen tissue, FFPE sections, blood and plasma biofluids, single-cell suspensions, and isolated DNA or RNA extracts.

How Transparent Are the Analysis Pipelines?

Pepkio hands over the raw R and Python scripts, exact parameter settings, and statistical filtering thresholds used in the analysis. Software tool versions and parameters are documented in the final deliverables.

Excelra documents software tool names, reference assemblies, statistical models, and parameter choices within final PDF/HTML reports and the OP² platform interface. Internal pipeline code parameters are formatted for executive reporting and cloud portal visualization.

How Do Code Delivery and Reproducibility Compare?

Pepkio delivers executable R and Python code, so researchers can inspect script logic, modify thresholds, and rerun analyses on local workstations. Pepkio also offers optional Nextflow or Snakemake pipeline files and Docker or Conda environment configurations.

Excelra delivers processed data matrices, summary tables, static reports, and interactive web views through the OP² portal. Raw executable code delivery or custom pipeline development is primarily provided under custom workflow engineering or FTE consulting contracts.

What Publication and Reviewer Support Is Provided?

Both providers support manuscript drafting and peer review. Pepkio delivers editable vector graphics (SVG, PDF) for custom formatting, a draft Methods text covering tools and parameters, and bioinformatician assistance to perform re-analyses requested by journal reviewers.

Excelra provides publication-ready static figures (SVG, PDF, PNG) alongside interactive web visualizations, structured methodology text with tool citations, and scientific consulting support to clarify analytical models during peer review.

What Are the Turnaround Times?

Pepkio typically completes standard cohort studies within 2 to 4 weeks, with complex multi-contrast projects taking 4 to 6 weeks. Turnaround schedules are set during upfront scoping.

Excelra uses automated execution timelines for standard NGS runs via OP². Custom multi-omics integration, AI model training, and drug discovery FTE projects operate on multi-week to multi-month milestone schedules agreed during project scoping.

How Do Communication Models Compare?

Pepkio connects researchers with the lead computational biologist working on their project throughout scoping, analysis, and post-delivery review. Communication occurs via email and video teleconferences.

Excelra assigns scientific project leads, lead bioinformaticians, and computational biologists to participate in scoping calls, technical milestone reviews, and final results discussions via email and video teleconferences.

How Does Pricing Work?

Neither service posts fixed public price lists on their website. Pepkio quotes fixed project prices scoped per study, which include data processing, executable script handover, vector figures, Methods drafting, and reviewer support.

Excelra uses a quote-only commercial model offering project-based Fee-for-Service (FFS), Full-Time Equivalent (FTE) staffing retainers, and subscriptions to proprietary databases (GOSTAR, GOBIOM).

How Is Data Security and Compliance Handled?

Both providers operate under client data privacy standards where customer data, biological discoveries, and client-funded IP remain customer-owned. Pepkio retains no rights to client datasets or delivered scripts.

Excelra maintains information security standards including ISO 27001 and HIPAA certifications alongside GDPR alignment. Excelra retains background IP for its internal databases (GOSTAR, GOBIOM) and OP² platform architecture.

How Are Custom Analyses Handled?

Pepkio handles custom analytical requests, such as specialized contrast matrices, custom single-cell filtering, or custom figure layouts, through discussions with the assigned bioinformatician.

Excelra handles complex or non-standard analytical requirements, such as custom AI/ML model development, heterogeneous omics data integration, or target prioritization pipelines, through dedicated FTE consulting agreements or custom Statements of Work.

When Pepkio Is the Better Fit

• You need executable R or Python scripts to rerun, inspect, or modify analysis logic on your local machine.
• You require optional containerized environments (Docker/Conda) or workflow manager scripts (Nextflow/Snakemake) to integrate into internal pipelines.
• You want ongoing communication with the specific bioinformatician analyzing your dataset.
• You need editable vector graphics (SVG, PDF), a draft Methods section, and analyst assistance for peer-review revisions.
• You are seeking a fixed-quote project price for an academic manuscript or discrete omics study.

When Excelra Is the Better Fit

• Your project requires computational drug discovery services, such as target identification, mechanism of action (MoA) modeling, SAR modeling, or HLA typing.
• You need dedicated Full-Time Equivalent (FTE) computational biology staffing to support ongoing biopharma R&D operations.
• You want interactive web portal access (OP² platform) for non-coding team members to explore filterable tables and interactive plots.
• Your study involves multi-omics integration combining transcriptomics with mass spectrometry LC-MS/MS proteomics, metabolomics, or lipidomics.
• You require access to curated domain databases like GOSTAR (medicinal chemistry) or GOBIOM (biomarkers).

Trade-Offs at a Glance

Frequently Asked Questions

Do I get the actual R or Python scripts used for my data analysis?

Pepkio delivers executable R and Python scripts along with parameter logs and optional Docker/Conda or Nextflow/Snakemake files for local reruns. Excelra delivers interactive OP² platform views, summary reports, and processed data tables. Raw executable scripts from Excelra are primarily provided under custom workflow engineering or FTE agreements.

Can non-coding researchers explore analysis results interactively?

Excelra provides access to their cloud-based OP² (Online Pipeline Platform) portal, which allows team members without programming experience to filter tables, view interactive plots, and examine QC metrics. Pepkio provides processed data matrices and high-resolution figures, and hands over script files for computational team members to run locally.

Will either service write the Methods section for my paper?

Pepkio provides a draft publication-ready Methods section describing reference assemblies, alignment tools, statistical cutoffs, and software packages. Excelra includes structured methodology text, tool citations, parameter notes, and analytical descriptions within final deliverables that can be adapted into manuscript Methods sections.

How is peer-review support handled if journal reviewers request extra analyses?

Pepkio offers support where the computational biologist who ran your study helps draft responses, adjust parameter thresholds, or execute requested re-analyses. Excelra provides post-project consulting from their scientific and bioinformatics teams to help explain statistical models, clarify analytical choices, and answer reviewer questions.

What raw data formats do both providers accept?

Both accept platform-agnostic raw sequencing and omics files, including FASTQ files (Illumina, PacBio, Oxford Nanopore), aligned BAM/CRAM files, VCF variant files, gene expression matrices, microarray data, mass spectrometry files, and Olink quantification tables.

Do I need a subscription to use these bioinformatics services?

Pepkio operates on a study-by-study fixed-quote basis with no recurring subscription fees. Excelra offers project-based Fee-for-Service (FFS) pricing, dedicated FTE retainers for ongoing research, and enterprise subscription licensing for proprietary databases like GOSTAR and GOBIOM.

Who owns the intellectual property and analyzed data?

Both services treat customer data, biological discoveries, and client-funded IP as client-owned. Excelra retains background IP for its pre-existing internal databases (GOSTAR, GOBIOM) and OP² platform architecture.

Can both providers process single-cell RNA-seq and spatial transcriptomics datasets?

Pepkio analyzes single-cell RNA-seq and spatial transcriptomics (10x Visium/Visium HD), delivering clustering, cell-type annotation, and trajectory scripts. Excelra processes scRNA-seq (CellRanger, Seurat, Scanpy) and spatial transcriptomics datasets, providing cell-type classification, heterogeneity profiling, and interactive OP² visualization.

How do turnaround times compare between the two options?

Pepkio typically completes standard cohort studies in 2 to 4 weeks, with complex multi-contrast projects taking 4 to 6 weeks. Excelra provides automated timelines for standard NGS pipeline runs via OP², while custom multi-omics integration and FTE computational projects run on multi-week to multi-month milestone schedules agreed during scoping.

What options exist if my lab needs ongoing bioinformatics staffing rather than a single project?

Pepkio handles ongoing work through successive fixed-scope project quotes with dedicated analyst continuity. Excelra offers formal Full-Time Equivalent (FTE) retainer models, allowing organizations to contract dedicated computational biologists, biocurators, or AI specialists as an extended R&D team.

Bottom Line

If your lab needs dry-lab sequencing analysis with executable R and Python scripts, parameter logs, editable vector figures, and access to the bioinformatician, Pepkio may be the better fit. If your organization needs computational drug discovery, SAR modeling, multi-omics biocuration, interactive web portal dashboards, or dedicated FTE staffing, Excelra may be the better fit.