loading
LiteratureBiomedical imagesGene informationOthers


GENOMICS SOFTWARE


Show as: Icons - List - Order by: Novelty - Popularity - Name
Share:
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)

...continue to read
ProDeGe. Protocol for Decontamination of Genomes logo
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.

...continue to read
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

...continue to read
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.

...continue to read
VarSifter logo
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.

...continue to read
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.

...continue to read
PLINK - Whole genome association analysis toolset logo
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

...continue to read
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.

...continue to read
MultiMiR Database logo
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

...continue to read
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

...continue to read
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).

...continue to read
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

...continue to read
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

...continue to read
PyClone logo
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).

...continue to read
Page: 1 2



We use cookies. By browsing our site you agree to our use of cookies. Accept cookies Find out more