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http://adacgh.bioinfo.cnio.es/
A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/
Proper citation: ADaCGH (RRID:SCR_010916) Copy
http://www.genomics.agilent.com/en/product.jsp?cid=AG-PT-111&tabId=AG-PR-1017&_requestid=587725
Software for a complete CGH and CGH+SNP microarray data analysis and data reporting solution to streamline the day-to-day cytogenetic sample analysis research workflow.
Proper citation: Agilent CytoGenomics software (RRID:SCR_010917) Copy
An R package for analyzing large Affymetrix data sets.
Proper citation: Aroma.affymetrix (RRID:SCR_010919) Copy
http://code.google.com/p/diffreps/
Finding differential chromatin modification sites from ChIP-seq data.
Proper citation: diffReps (RRID:SCR_010873) Copy
http://www.webcitation.org/getfile?fileid=c6d148fcb4fde0ea6991ec319a7a3925d38f32bf
A software program which finds sequence elements conserved in a set of DNA sequences.
Proper citation: AlignACE (RRID:SCR_010875) Copy
http://sourceforge.net/p/arpeggio/wiki/Home/
Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.
Proper citation: Arpeggio (RRID:SCR_010876) Copy
http://autosome.ru/dichipmunk/
Software for motif discovery using dinucleotide position weight matrices (PWMs).
Proper citation: diChIPMunk (RRID:SCR_010879) Copy
A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations.
Proper citation: kmer-SVM (RRID:SCR_010882) Copy
http://bioinfo.au.tsinghua.edu.cn/software/NURD/
An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: NURD (RRID:SCR_010988) Copy
An agency responsible for the evaluation and supervision of medicines developed by pharmaceutical companies for use in the European Union. Its main responsibility is the protection and promotion of public and animal health through the evaluation and supervision of medicines for human and veterinary use. The Agency also plays a role in stimulating innovation and research in the pharmaceutical sector. The Agency gives scientific advice and other assistance to companies for the development of new medicines. It publishes guidelines on quality-, safety- and efficacy-testing requirements. A dedicated SME Office provides special assistance to small and medium-sized enterprises.
Proper citation: European Medicines Agency (RRID:SCR_011215) Copy
http://www.cisd.ethz.ch/software/openBIS
Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics
Proper citation: openBIS (RRID:SCR_011815) Copy
http://www.ebi.ac.uk/Tools/msa/kalign/
A fast and accurate multiple sequence alignment algorithm.
Proper citation: Kalign (RRID:SCR_011810) Copy
http://mafft.cbrc.jp/alignment/server/
Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
Proper citation: MAFFT (RRID:SCR_011811) Copy
http://wishart.biology.ualberta.ca/cgview/
A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CGView (RRID:SCR_011779) Copy
http://bioen-compbio.bioen.illinois.edu/PSAR-Align/
Software for improving multiple sequence alignment using probabilistic sampling.
Proper citation: PSAR-Align (RRID:SCR_011814) Copy
http://gaggle.systemsbiology.net/docs/geese/genomebrowser/
An open source software tool for visualizing high-density data plotted against coordinates on the genome.
Proper citation: Gaggle (RRID:SCR_011780) Copy
http://www.csd.uwo.ca/~ilie/HiTEC/
Accurate error correction in high-throughput sequencing data.
Proper citation: HiTEC (RRID:SCR_011826) Copy
https://bioinf.eva.mpg.de/patman/
Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PatMaN (RRID:SCR_011821) Copy
http://bix.ucsd.edu/projects/hammer/
A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Hammer (RRID:SCR_011825) Copy
http://www.g-language.org/GenomeProjector/
A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.
Proper citation: Genome Projector (RRID:SCR_011790) Copy
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