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GENOMICS SOFTWARE


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AltAnalyze logo
AltAnalyze
Category: DNA microarray software, Genomics software

AltAnalyze is an easy-to-use application for microarry and RNA-Seq analysis. For splicing sensitive platforms, AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for conventional arrays (RMA summarization, QC, statistics, annotation, clustering, lineage characterization and gene-set enrichement).

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AnnoVar logo
AnnoVar
Category: Genomics software

ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others).ANNOVAR is written in Perl and can be run as a standalone application on diverse hardware systems where standard Perl modules are installed.

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Argo Genome Browser logo
Argo Genome Browser
Category: Genomics software
Subcategories: Broad

The Argo Genome Browser is the Broad Institute's production tool for visualizing and manually annotating whole genomes. It's a free and open source standalone Java 1.4 application.

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ArrayOligoSelector logo
ArrayOligoSelector
Category: Genomics software

ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.

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Bifido Punnett Square Calculator logo
Bifido Punnett Square Calculator
useful and fast genetic calculator
Category: Genomics software

This is useful and fast genetic calculator for predicting the offspring results of genetic crosses. The application can show all possible allelic combinations of gametes and produce genotypes and phenotypes ratio and probability for these crosses. You can easily generate punnett squares with unlimited number of genes and results will be ready in less than one second due to unique algorithms of this calculator. The complete accuracy of these results we can guarantee. From now punnett squares calc

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Bioconductor logo
Bioconductor
Category: Genomics software, DNA microarray software

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language and most bioconductor components are distributed as R packages, which are add-on modules for R. It is open source and open development. Boconductor core team is based primarily at the Fred Hutchinson Cancer Research Center (http://en.wikipedia.org/wiki/Bioconductor)

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Bionimbus logo
Bionimbus
Category: Genomics software

The Bionimbus Protected Data Cloud (PDC), developed at the University of Chicago, is an open-source cloud-based infrastructure for managing, analyzing, and sharing large amounts of genomics and phenotypic data in a secure and compliant manner. Bionimbus is part of a larger project called the Open Science Data Cloud (OSDC) and there is a version of Bionimbus (Bionimbus Community Cloud) for open-access data and a version for controlled-access data (Bionimbus PDC). Bionimbus is based primarily upon

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Circos logo
Circos
Category: Genomics software

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. Although originally designed for visualizing genomic data, it can create figures from data in any field. It requires PERL software language.

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DAGchainer logo
DAGchainer
Category: Genomics software

The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts for the distance between neighboring genes on each DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs are computed and reported. This algorithm can be used to mine large evolutionary conserved regi

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Eisen Lab Software logo
Eisen Lab Software
Genomics software tools
Category: Genomics software

We are not a software development lab, but we develop a lot of software tools to support our research and make it all available for anyone to use and repurpose.

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Exomiser logo
Exomiser
Category: Genomics software
Subcategories: Sanger

The Exomiser is a Java applicationthat that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. It is an opensource Java software package that can be downloaded and run on a single desktop computer. It filters and prioritizes candidate genes and variants from whole-exome or wholegenome sequencing data, with a special focus on phenotypic data. Users enter a patient’s clinical features and exome into the program, and Exomiser generates a scored list of cand

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Galaxy logo
Galaxy
Category: Genomics software

Galaxy is an open, web-based platform for data intensive biomedical research, now available as a "cloud computing" resource Whether on this free public server or your own instance, you can perform, reproduce, and share complete analyses.

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GenePattern logo
GenePattern
Category: Genomics software, Proteomics software

GenePattern is a powerful genomic analysis platform that provides access to more than 150 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

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GERP logo
GERP
Category: Genomics software

Genomic Evolutionary Rate Profiling (GERP) identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as "Rejected Substitutions".

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Gerstein Lab Structural & Copy Number Variations logo
Gerstein Lab Structural & Copy Number Variations
Category: Genomics software

A portal collecting several downloadable tools for the study of genomic structural & copy number variations. Software tools can be used to construct a personal diploid genome sequence by including personal variants into reference genome (vcf2diploid), to discover and genotype CNVs from genome sequencing (CNVnator), etc.

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Glimmer logo
Glimmer
Category: Genomics software

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.

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GSEA logo
GSEA
Gene Set Enrichment Analysis
Category: Genomics software

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

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Infernal logo
Infernal
Category: Genomics software

Infernal (inference of RNA alignments) is a software package for searching DNA sequence databases for RNA structure and sequence similarities. It allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments.

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Integrative Genomics Viewer (IGV) logo
Integrative Genomics Viewer (IGV)
Category: Genomics software

The Integrated Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations.

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JaMBW 1.1 logo
JaMBW 1.1
Category: Genomics software

JaMBW, the Java based Molecular Biologist's Workbench, is an online platform that had been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has. The peculiar aspect of JaMBW, however, is to take advantage of the foremost developments in computer science in order to deliver information in a way simple to use.

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