GENOMICS SOFTWARE

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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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JBrowse

The JBrowse Genome Browser

Category: Gene expression, Genomics software

JBrowse is a fast and full-featured scalable genome browser built completely with JavaScript and HTML5. It can run on your desktop, or be embedded in your website (see Bues et al., Genome Biol 17, 66 (2016) doi:10.1186/s13059-016-0924-1).

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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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ProDeGe. Protocol for Decontamination of Genomes

Category: Genomics software

ProDeGe is the first fully automated computational protocol for decontamination of genomes. The protocol uses public databases to detect contamination in agenome assembly, then groups contigs into “Clean” or “Contaminant” groups. ProDeGe spits out lists that users can read through to identify contaminants and determine what they mightbe.The standalone software is freely available and can be run on any system that has Perl, R, Prodigal and NCBI Blast installed. (Tennessen et al., ISME J.

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PLINK - Whole genome association analysis toolset

Category: Genomics software

PLINK is a popular and computationally efficient software program that offers a comprehensive and well-documented set of automated genome wide association quality control and analysis tools. It is a freely available open source software written in C++, which can be installed on Windows, Mac and Unix machines. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from ra

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PyClone

Category: Genomics software

PyClone is a tool for inferring the cellular prevalence of point mutations from deeply sequenced data. It serves as a statistical model for inference of clonal population structures in cancers.The model supports simultaneous analysis of multiple related samples and infers clusters of mutations whose cellular prevalences shift together. Such clusters of mutations can be inferred as mutational genotypes of distinct clonal populations (Roth et al., Nature Meth 11, 396, 2014).

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MultiMiR Database

Category: Genomics software

The R package multiMiR, with web server is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs. Within this database, investigators can find clues to potential new treatments for various diseases, including cancer. In addition to helping researchers search for relationships between microRNAs and their genetic targets, multiMiR includes drugs that affect these microRNAs and lists associated diseases.The database combines n

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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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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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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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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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VarSifter

Category: Genomics software

VarSifter is a graphical Java program designed to display, sort, filter, and generally sift variation data from massively parallel sequencing experiments. It is designed to read exome-scale variation data in either a tab-delimited text file with header, or an uncompressed VCF file. The program is written in Java, and should run on any platform with a current Java Virtual Machine.

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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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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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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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VAAST

Category: Genomics software

VAAST (the Variant Annotation, Analysis and Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases.

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PROVEAN

Category: Genomics software

PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important. The performance of PROVEAN is comparable to popular tools such as SIFT or PolyPhen-2.

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PHAST

Category: Genomics software

PHAST is a freely available software package (Cornell University) for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel).Like algorithms that assess protein-coding genes, they evaluate variants on the basis of how often the sequence changes between species

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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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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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