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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
http://emboss.sourceforge.net/
Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication.
Proper citation: EMBOSS (RRID:SCR_008493) 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
http://lowelab.ucsc.edu/tRNAscan-SE
Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file).
Proper citation: tRNAscan-SE (RRID:SCR_008637) 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
http://cran.r-project.org/web/packages/DWD/
This software package provides the implementation of distance weighted discrimination (DWD) using an interior point method for the solution of second order cone programming problems.
Proper citation: DWD (RRID:SCR_008760) Copy
An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.
Proper citation: RUM (RRID:SCR_008818) Copy
https://github.com/hangelwen/miR-PREFeR
An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.
Proper citation: miR-PREFeR (RRID:SCR_003353) Copy
An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets
Proper citation: PicTar (RRID:SCR_003343) Copy
https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust
Software for efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.
Proper citation: BlockClust (RRID:SCR_003347) Copy
http://www.bioconductor.org/packages/release/bioc/html/EasyqpcR.html
Software package for low-throughput real-time quantitative PCR data analysis. The package allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors.
Proper citation: EasyqpcR (RRID:SCR_003406) Copy
https://planttfdb.gao-lab.org/
Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
Proper citation: PLANTTFDB (RRID:SCR_003362) Copy
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