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http://jexpress.bioinfo.no/site/
Gene expression analysis software using Java.
Proper citation: J-Express (RRID:SCR_003609) Copy
Software for identifying haplogroups from low coverage sequence data.
Proper citation: YHap (RRID:SCR_007951) Copy
https://code.google.com/p/ampliconnoise/
A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.
Proper citation: AmpliconNoise (RRID:SCR_007814) Copy
http://web1.sph.emory.edu/users/hwu30/polyaPeak.html
An R package for ranking ChIP-seq peaks with shape information.
Proper citation: polyaPeak (RRID:SCR_007687) Copy
https://sites.google.com/site/dadadenoiser/
Infers both the sample genotypes and error parameters that produced a metagenome data set.
Proper citation: DADA (RRID:SCR_008205) Copy
Software package that contains a collection of statistical tools for analysing RNA-seq expression data.
Proper citation: MMSEQ (RRID:SCR_008184) Copy
A cloud platform for next-generation sequencing analysis.
Proper citation: Seven Bridges Genomics (RRID:SCR_008308) Copy
http://epicenter.immunbio.mpg.de/services/chromos/
Combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect.
Proper citation: ChroMoS (RRID:SCR_008320) Copy
http://bioinfo-out.curie.fr/projects/vamp/
Software for visualization and Analysis of CGH arrays, transcriptome and other Molecular Profiles.
Proper citation: VAMP (RRID:SCR_008527) Copy
http://www.bioconductor.org/packages/2.6/bioc/html/DEGseq.html
R package to identify differentially expressed genes from RNA-Seq data.
Proper citation: DEGseq (RRID:SCR_008480) Copy
The directing and coordinating authority responsible for public health within the United Nations system. The WHO Regional Office for Europe (WHO/Europe) is one of the six regional offices around the world. It serves the WHO European Region, which comprises 53 countries from the Atlantic to the Pacific oceans. WHO/Europe collaborates with a range of public health stakeholders in the Region and globally, to ensure that coordinated action is taken to develop and implement efficient health policies and to strengthen health systems. WHO/Europe is made up of public health, scientific, and technical experts.
Proper citation: World Health Organization (RRID:SCR_008505) Copy
https://sites.google.com/site/drivermutationidentification/
Computational tool developed to help identify cancer-associated ''driver'' mutations from ''passenger'' ones in a cancer genome.
Proper citation: DMI (RRID:SCR_008599) Copy
Ratings or validation data are available for this resource
http://www.ingenuity.com/products/pathways_analysis.html
A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest.
Proper citation: Ingenuity Pathway Analysis (RRID:SCR_008653) Copy
A robust, secure, medical-grade, web application that lives in the cloud and has the ability to analyze and annotate entire human genomes in a rapid and cost-effective way.
Proper citation: Tute Genomics (RRID:SCR_008672) Copy
http://homes.esat.kuleuven.be/~bioiuser/eXtasy/
A pipeline for ranking nonsynonymous single nucleotide variants given a specific phenotype.
Proper citation: eXtasy (RRID:SCR_008671) Copy
A method to assess the outcome of nonsynonymous SNVs using a consensus deleteriousness score that combines various tools (e.g. SIFT, Polyphen2, MutationAssessor).
Proper citation: Condel (RRID:SCR_008584) Copy
A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
Proper citation: Minia (RRID:SCR_004986) Copy
http://compbio.cs.huji.ac.il/NucPosition/TemplateFiltering/Home.html
A software pipeline for analyzing deep sequencing maps of chromatin structure.
Proper citation: TemplateFilter (RRID:SCR_004980) Copy
An Operational Taxonomic Unit (OTU) clustering software for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures.
Proper citation: UPARSE (RRID:SCR_005020) Copy
http://www.cebitec.uni-bielefeld.de/index.php/2-uncategorised/47-carma?highlight=WyJjYXJtYSJd
A software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system.
Proper citation: CARMA (RRID:SCR_004999) Copy
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