ncibtep@nih.gov

Bioinformatics Training and Education Program

Scientific Software

The resources listed below are software packages that have been used for the BTEP training classes. This list contains both commercial and open source software.  (Clicking on the images will provide additional details about the software).

Biodiscovery Nexus Software

Biodiscovery Nexus Software

Biodiscovery Nexus Software

Software that offers simple yet powerful tools for copy number (CNV) and sequence variation analysis and visualization from aCGH, SNP arrays as well as NGS WES/WGS and expression ...
cBioPortal

cBioPortal

cBioPortal

The cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. The cBioPortal significantly lowers the barriers between complex genomic data and ...
Cytoscape

Cytoscape

Cytoscape

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
EasyPanel

EasyPanel

EasyPanel

Intelligent and automated flow cytometry panel designer for traditional and spectral cytometers
Geneious Prime

Geneious Prime

Geneious Prime

Geneious Prime is desktop bioinformatics software that is both ultra-powerful and easy to use. Scientists are able to search, organize, and analyze genomic and protein data.
Integrative Genomics Viewer

Integrative Genomics Viewer

Integrative Genomics Viewer

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. One favorite use is inspection of alignments to rule out alignment artifacts resulting in false-postive variant calls.
NDEx

NDEx

NDEx

NDEx provides a commons where the rapidly expanding corpus of biological network models created by researchers can be shared, discussed, reviewed, and used. It is public forum where biologists can ...
NIH Helix/Biowulf

NIH Helix/Biowulf

NIH Helix/Biowulf

The Helix/Biowulf system is an invaluable resource for the CCR bioinformatics community. Not only does is provide access to state of the art hardware, with huge computing capacity, but ...
Partek Flow

Partek Flow

Partek Flow

Partek Flow (Partek) is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data.
Partek Genomics Suite

Partek Genomics Suite

Partek Genomics Suite

Partek Genomics Suite is a comprehensive suite for advanced statistics and interactive data visualization, specifically designed to reliably extract biological signals from noisy data.
QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench

QIAGEN CLC Workbench is a user-friendly solution for DNA, RNA and protein data sequence analysis. It houses tools for molecular biology and next generation sequencing (NGS) data analysis.
QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

QIAGEN  Ingenuity Pathway Analysis (IPA) works with differential expression data (NGS, microarray, proteomics, and others) or genetic variant data to extract various biological insights.
Qlucore Omics Explore

Qlucore Omics Explore

Qlucore Omics Explore

Qlucore Omics Explorer (Qlucore) is a graphical user interface (GUI) package used for 'omics data analysis. This software can analyze many different types of 'omics data when ...
R Studio

R Studio

R Studio

Rstudio is the ideal Desktop client for those interested in getting started with R.
SnapGene

SnapGene

SnapGene

SnapGene is a point and click proprietary software program used for designing and documenting molecular biology experiments. SnapGene is a multipurpose software program.
UCSC Genome Browser

UCSC Genome Browser

UCSC Genome Browser

The UCSC Genome Browser is the "goto tool" for viewing sequence data in a genomic context. It's wide variety of supported organisms and data types, coupled with its responsive performance ...
UCSC Xena Browser

UCSC Xena Browser

UCSC Xena Browser

UCSC Xena Functional Genomics Browser is an open-source, web-based tool for analytics and visualization of viewing the public data hubs. Xena also allows securely analysis and visualization of your private ...
Biodiscovery Nexus Software

Biodiscovery Nexus Software

Biodiscovery Nexus Software

Software that offers simple yet powerful tools for copy number (CNV) and sequence variation analysis and visualization from aCGH, SNP arrays as well as NGS WES/WGS and expression ...
EasyPanel

EasyPanel

EasyPanel

Intelligent and automated flow cytometry panel designer for traditional and spectral cytometers
Geneious Prime

Geneious Prime

Geneious Prime

Geneious Prime is desktop bioinformatics software that is both ultra-powerful and easy to use. Scientists are able to search, organize, and analyze genomic and protein data.
Partek Flow

Partek Flow

Partek Flow

Partek Flow (Partek) is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data.
Partek Genomics Suite

Partek Genomics Suite

Partek Genomics Suite

Partek Genomics Suite is a comprehensive suite for advanced statistics and interactive data visualization, specifically designed to reliably extract biological signals from noisy data.
QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench

QIAGEN CLC Workbench is a user-friendly solution for DNA, RNA and protein data sequence analysis. It houses tools for molecular biology and next generation sequencing (NGS) data analysis.
QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

QIAGEN  Ingenuity Pathway Analysis (IPA) works with differential expression data (NGS, microarray, proteomics, and others) or genetic variant data to extract various biological insights.
Qlucore Omics Explore

Qlucore Omics Explore

Qlucore Omics Explore

Qlucore Omics Explorer (Qlucore) is a graphical user interface (GUI) package used for 'omics data analysis. This software can analyze many different types of 'omics data when ...
SnapGene

SnapGene

SnapGene

SnapGene is a point and click proprietary software program used for designing and documenting molecular biology experiments. SnapGene is a multipurpose software program.
cBioPortal

cBioPortal

cBioPortal

The cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. The cBioPortal significantly lowers the barriers between complex genomic data and ...
Integrative Genomics Viewer

Integrative Genomics Viewer

Integrative Genomics Viewer

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. One favorite use is inspection of alignments to rule out alignment artifacts resulting in false-postive variant calls.
QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

QIAGEN  Ingenuity Pathway Analysis (IPA) works with differential expression data (NGS, microarray, proteomics, and others) or genetic variant data to extract various biological insights.
UCSC Genome Browser

UCSC Genome Browser

UCSC Genome Browser

The UCSC Genome Browser is the "goto tool" for viewing sequence data in a genomic context. It's wide variety of supported organisms and data types, coupled with its responsive performance ...
UCSC Xena Browser

UCSC Xena Browser

UCSC Xena Browser

UCSC Xena Functional Genomics Browser is an open-source, web-based tool for analytics and visualization of viewing the public data hubs. Xena also allows securely analysis and visualization of your private ...
Biodiscovery Nexus Software

Biodiscovery Nexus Software

Biodiscovery Nexus Software

Software that offers simple yet powerful tools for copy number (CNV) and sequence variation analysis and visualization from aCGH, SNP arrays as well as NGS WES/WGS and expression ...
Cytoscape

Cytoscape

Cytoscape

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
Geneious Prime

Geneious Prime

Geneious Prime

Geneious Prime is desktop bioinformatics software that is both ultra-powerful and easy to use. Scientists are able to search, organize, and analyze genomic and protein data.
Integrative Genomics Viewer

Integrative Genomics Viewer

Integrative Genomics Viewer

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. One favorite use is inspection of alignments to rule out alignment artifacts resulting in false-postive variant calls.
NDEx

NDEx

NDEx

NDEx provides a commons where the rapidly expanding corpus of biological network models created by researchers can be shared, discussed, reviewed, and used. It is public forum where biologists can ...
Partek Flow

Partek Flow

Partek Flow

Partek Flow (Partek) is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data.
QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench

QIAGEN CLC Workbench is a user-friendly solution for DNA, RNA and protein data sequence analysis. It houses tools for molecular biology and next generation sequencing (NGS) data analysis.
Qlucore Omics Explore

Qlucore Omics Explore

Qlucore Omics Explore

Qlucore Omics Explorer (Qlucore) is a graphical user interface (GUI) package used for 'omics data analysis. This software can analyze many different types of 'omics data when ...
R Studio

R Studio

R Studio

Rstudio is the ideal Desktop client for those interested in getting started with R.
SnapGene

SnapGene

SnapGene

SnapGene is a point and click proprietary software program used for designing and documenting molecular biology experiments. SnapGene is a multipurpose software program.
cBioPortal

cBioPortal

cBioPortal

The cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. The cBioPortal significantly lowers the barriers between complex genomic data and ...
Cytoscape

Cytoscape

Cytoscape

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
Integrative Genomics Viewer

Integrative Genomics Viewer

Integrative Genomics Viewer

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. One favorite use is inspection of alignments to rule out alignment artifacts resulting in false-postive variant calls.
NDEx

NDEx

NDEx

NDEx provides a commons where the rapidly expanding corpus of biological network models created by researchers can be shared, discussed, reviewed, and used. It is public forum where biologists can ...
R Studio

R Studio

R Studio

Rstudio is the ideal Desktop client for those interested in getting started with R.
UCSC Genome Browser

UCSC Genome Browser

UCSC Genome Browser

The UCSC Genome Browser is the "goto tool" for viewing sequence data in a genomic context. It's wide variety of supported organisms and data types, coupled with its responsive performance ...
UCSC Xena Browser

UCSC Xena Browser

UCSC Xena Browser

UCSC Xena Functional Genomics Browser is an open-source, web-based tool for analytics and visualization of viewing the public data hubs. Xena also allows securely analysis and visualization of your private ...
cBioPortal

cBioPortal

cBioPortal

The cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. The cBioPortal significantly lowers the barriers between complex genomic data and ...
Cytoscape

Cytoscape

Cytoscape

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
Geneious Prime

Geneious Prime

Geneious Prime

Geneious Prime is desktop bioinformatics software that is both ultra-powerful and easy to use. Scientists are able to search, organize, and analyze genomic and protein data.
Integrative Genomics Viewer

Integrative Genomics Viewer

Integrative Genomics Viewer

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. One favorite use is inspection of alignments to rule out alignment artifacts resulting in false-postive variant calls.
NDEx

NDEx

NDEx

NDEx provides a commons where the rapidly expanding corpus of biological network models created by researchers can be shared, discussed, reviewed, and used. It is public forum where biologists can ...
Partek Flow

Partek Flow

Partek Flow

Partek Flow (Partek) is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data.
Qlucore Omics Explore

Qlucore Omics Explore

Qlucore Omics Explore

Qlucore Omics Explorer (Qlucore) is a graphical user interface (GUI) package used for 'omics data analysis. This software can analyze many different types of 'omics data when ...
R Studio

R Studio

R Studio

Rstudio is the ideal Desktop client for those interested in getting started with R.
SnapGene

SnapGene

SnapGene

SnapGene is a point and click proprietary software program used for designing and documenting molecular biology experiments. SnapGene is a multipurpose software program.
UCSC Genome Browser

UCSC Genome Browser

UCSC Genome Browser

The UCSC Genome Browser is the "goto tool" for viewing sequence data in a genomic context. It's wide variety of supported organisms and data types, coupled with its responsive performance ...
UCSC Xena Browser

UCSC Xena Browser

UCSC Xena Browser

UCSC Xena Functional Genomics Browser is an open-source, web-based tool for analytics and visualization of viewing the public data hubs. Xena also allows securely analysis and visualization of your private ...
NIH Helix/Biowulf

NIH Helix/Biowulf

NIH Helix/Biowulf

The Helix/Biowulf system is an invaluable resource for the CCR bioinformatics community. Not only does is provide access to state of the art hardware, with huge computing capacity, but ...
R Studio

R Studio

R Studio

Rstudio is the ideal Desktop client for those interested in getting started with R.