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Getting Started with OmicSoft

Welcome to the OmicSoft Onboarding portal.


Start here for quick info to help you get started with the key capabilities, but don't hesitate to reach out to ts-bioinformatics@qiagen.com for help.

OmicSoft Suite provides powerful bioinformatics workflows and visualizations, and access to a massive collection of deeply-curated disease and oncology omics data sets.

Quick navigation tabs at the top of the page provide information targeted for New users, Power users, Developers and License Administrators.

Go to quick start links



Use OmicSoft to quickly look up gene expression patterns across disease and normal tissue, or visualize pre-analyzed internal data in OmicSoft Studio.

Use OmicSoft Studio's advanced analysis and visualizations for internal and public data exploration, for their work and to support biologists.

Use OmicSoft's curated Lands datasets exported as flat files or via APIs, and interact with OmicSoft Server using custom scripts and pipelines.

Manage access for new users, and coordinate custom end-user trainings with QIAGEN.

Getting started

Getting started with OmicSoft

Key Resources

Information for the Biologist | Occasional or new user

Learn about: Quickly finding and visualizing data for your area of research, basic analysis steps, introductory videos, internal resources


Disease Biomarker Discovery Quick biomarker discovery from thousands of deeply-curated omics datasets for disease and normal tissue, using QIAGEN OmicSoft DiseaseLand

Oncology Biomarker Discovery Quick biomarker discovery from Oncology-focused datasets for exploration, including TCGA, CCLE, TARGET, and thousands of GEO studies, using QIAGEN OmicSoft OncoLand

Omics data analysis Basic omics analysis and statistics capabilities of OmicSoft Studio, such as RNA-seq, microarray, RT-PCR, differential expression

Disease Biomarker Discovery
Accelerate disease-focused target discovery with DiseaseLand, by exploring thousands of curated studies with expression data, extensive metadata, and precomputed comparisons from each study revealing differential expression between Treated vs Control, Disease vs Normal, Responder vs Non-Responder, and more.

Learn how to harness visualizations and powerful filters to answer omics-related questions.

Introduction

Introduction to DiseaseLand's curated datasets

Getting Started

Get started with exploring DiseaseLand data

Advanced Topics

Websites, videos, documents on DiseaseLand to dive deeper into the data

Oncology Biomarker Discovery
Accelerate cancer-focused target discovery using OncoLand, with manually-curated and unified multi-omics datasets from consortia like TCGA, TARGET, GTEx, CCLE, and thousands of curated studies with expression data, extensive clinical metadata, and precomputed comparisons from each study revealing differential expression between Treated vs Control, Disease vs Normal, Responder vs Non-Responder, and more.

Learn how to harness visualizations and powerful filters to answer omics-related questions.

Introduction

Introduction to OncoLand

Getting Started

Getting started with OncoLand.

Advanced Topics

Websites, videos, documents on OncoLand

Use case demos

Examples that answer common scientific questions

Omic data analysis
OmicSoft Studio is a powerful interactive tool for omics data exploration, which works in connection with your OmicSoft Server. Common use cases include built-in NGS analyses, data visualization, and differential expression analysis.

Introduction

Getting started with Omic data analysis

Getting Started

Getting started with OmicSoft Analysis

Advanced Topics

In-depth resources of OmicSoft Omic data analysis

Information for the OmicSoft power user | Experienced User of OmicSoft Suite

Learn about advanced capabilities of the software, use cases, and videos


DiseaseLand Advanced exploration of thousands of deeply-curated omics datasets for disease and normal tissue, ready to use to identify biomarkers

OncoLand Advanced exploration of oncology-focused datasets for exploration, including TCGA, CCLE, TARGET, and thousands of GEO studies

Omic data analysis In-depth omics analysis and statistics capabilities of OmicSoft Studio, such as RNA-seq, microarray, RT-PCR, differential expression

DiseaseLand
DiseaseLand accelerates disease-focused target discovery by providing access to thousands of curated studies with expression data, extensive sample-level metadata, and precomputed comparisons from each study revealing differential expression between Treated vs Control, Disease vs Normal, Responder vs Non-Responder, and more. Learn how to harness visualizations, correlation analytics and data exports to answer omics-related questions.

Introduction

Introduction to DiseaseLand

Getting Started

Getting started with DiseaseLand

Advanced Topics

Websites, videos, documents on DiseaseLand

OncoLand
OncoLand accelerates cancer-focused target discovery by providing access to manually-curated and unified multi-omics datasets from consortia like TCGA, TARGET, GTEx, CCLE, and thousands of curated studies with expression data, extensive sample-level metadata, and precomputed comparisons from each study revealing differential expression between Treated vs Control, Disease vs Normal, Responder vs Non-Responder, and more. Learn how to harness visualizations and powerful filters generate custom comparisons within and between omics data types, and export custom datasets to answer advanced omics-related questions.

Introduction

Getting started with OncoLand

Getting Started

Getting started with OncoLand.

Advanced Topics

Websites, videos, documents on OncoLand

Use case demos

Examples that answer common scientific questions

Omic data analysis
OmicSoft Studio is a powerful desktop client for omics analysis that works in connection with OmicSoft Server. Advanced use cases of OmicSoft Studio include customized NGS and Omics analyses, visualizations built on advanced filtering, and complex differential gene regulation analyses.

Introduction

Introduction to Omic data analysis

Getting Started

Getting started with Omic data analysis

Advanced Topics

In-depth resources on Omic data analysis

Information for Data Scientist | Developer | programmatic/analytic user

Learn about Large data handling, access to full flat files, APIs, scripting, programming access using R and Python

Programmatic access to Lands data

Use flat files, APIs to explore thousands of deeply-curated omics datasets

1. Disease-focused datasets for disease and normal tissue, ready to use to identify biomarkers
2. Oncology-focused datasets, including TCGA, CCLE, TARGET, and thousands of GEO studies
3. Single cell transcriptomic datasets with full curation of project, sample, cluster, and cell data

Programmatic data analysis pipelines

Use scripting methods to submit analyses directly to OmicSoft Server for in-depth omics analysis

1. Analysis pipelines for RNA-seq, microarray, RT-PCR, differential expression and more

Information for the OmicSoft Server Admin | license manager | Software advocates

Learn about: General benefits and uses of OmicSoft software and data, successful implementation and basic usage

Basic administration tasks

User Management, data administration
  • Download and install OmicSoft Studio (website)
  • Publish new Cloud Lands (Video)

    When new "Land" databases are released, the OmicSoft Administrator should download these data to your server. Quarterly updates to existing databases are auto-downloaded and do not need routine maintenance.

  • Add/remove users on OmicSoft Server. (website)

    When a new user has followed the "Installation and quick start" document, the OmicSoft Administrator should add them to your OmicSoft Server with "Manage Users", unless your server uses LDAP or "no user authentication".

  • Update/Restart OmicSoft Server application. (website)

    To update your OmicSoft Server to the latest version, or to activate the latest license key, the OmicSoft Administrator must briefly stop and restart the server application.

General information

Read about instructions on OmicSoft Studio installation.

Additional Information

Read about introductory materials on OmicSoft Suite
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