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http://www.embl.de/~korbel/CopySeq/
A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.
Proper citation: CopySeq (RRID:SCR_010758) Copy
https://github.com/ekg/freebayes
A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.
Proper citation: FreeBayes (RRID:SCR_010761) Copy
https://code.google.com/p/balony/
Image analysis and data inspection software for agar plates generated in high-throughput yeast genetics and genomics experiments.
Proper citation: balony (RRID:SCR_010968) Copy
http://www.bioinformatics.org/oligofaktory/
A free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more��
Proper citation: OligoFaktory (RRID:SCR_010962) Copy
http://probemaker.sourceforge.net/
A Java software aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes.
Proper citation: ProbeMaker (RRID:SCR_010964) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 1, 2014, A web-based software tool that enables selecting optimal oligos for PCR applications and multiplex detection.
Proper citation: PROBEmer (RRID:SCR_010965) Copy
http://www.uhnresearch.ca/labs/tillier/ProDesign/ProDesign.html
Webserver that can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program.
Proper citation: ProDesign (RRID:SCR_010966) Copy
A Plant MicroRNA Target Expression Database to study the microRNA (miRNA) functions by inferring their target gene expression profiles among the large amount of existing microarray data. You may also predict your miRNA targets and retrieve their microarray expression data.
Proper citation: PMTED (RRID:SCR_010854) Copy
http://www.stat.wisc.edu/~chungdon/dpeak/
A high resolution transcription factor binding site (TFBS) identification (deconvolution) algorithm. dPeak implements a probabilistic model that accurately describes ChIP-exo and ChIP-Seq data generation process for both the SET and PET assays.
Proper citation: dPeak (RRID:SCR_010855) Copy
http://bioinfo-out.curie.fr/projects/micsa/
A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris).
Proper citation: MICSA (RRID:SCR_010860) Copy
http://ceas.cbi.pku.edu.cn/index.html
Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CEAS (RRID:SCR_010946) Copy
http://lgsun.grc.nia.nih.gov/ANOVA/
Data analysis server / software designed to test statistical significance of gene microarray data, visualize the results, and provide links to clone information and gene index. Several public datasets are also available.
Proper citation: NIA Array Analysis (RRID:SCR_010948) Copy
http://www.cebitec.uni-bielefeld.de/comics/index.php/emma
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 17, 2017. A MAGE-compliant software platform for the collaborative analysis and integration of microarray data.
Proper citation: EMMA2 (RRID:SCR_010940) Copy
http://sourceforge.net/projects/xdrawchem/
A drawing software application designed for drawing and analyzing chemical structures and reactions.
Proper citation: XDrawChem (RRID:SCR_010941) Copy
A microarray data warehouse integrated with a software platform for microarray data analysis. It can be used as a LIMS for DNA chip experiments, also. Unlike other microarray data repositories, it entirely dispenses with free-text format, instead holding all the information in a format ready for statistical analysis.
Proper citation: M-CHiPS (RRID:SCR_010944) Copy
http://genetics.emory.edu/research/?assetID=2087
A GUI software package for analysis of DNA methylation microarray data.
Proper citation: MethLAB (RRID:SCR_010957) Copy
http://rnbeads.bioinf.mpi-inf.mpg.de/
An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite sequencing protocols, but also MeDIP-seq and MBD-seq., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: RnBeads (RRID:SCR_010958) Copy
http://bioinfo.au.tsinghua.edu.cn/software/fastdma/
A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.
Proper citation: FastDMA (RRID:SCR_010954) Copy
A combined database and R package that allows you to investigate the methylation state of regions of interest across the genome.
Proper citation: Marmal-aid (RRID:SCR_010956) Copy
http://www.illumina.com/software/illumina_connect.ilmn
Software that estimates copy number and annotates regions with copy number variants(CNV).
Proper citation: CNVPartition (RRID:SCR_010925) Copy
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