Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

http://pmted.agrinome.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.mchips.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://marmal-aid.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/~giannoul/GenoSNP/

A genotyping algorithm for the Illumina Infinium SNP genotyping assay.

Proper citation: GenoSNP (RRID:SCR_010928) Copy   

•   Source: SciCrunch Registry

http://biogrid-head.engr.uconn.edu/lasagna_search/

An integrated web tool for transcription factor binding site search and visualization. Both the Python Scripts for Offline Scanning and the Python implementation of the LASAGNA algorithm are available., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LASAGNA-Search (RRID:SCR_010883) Copy   

•   Source: SciCrunch Registry

http://rsat.ulb.ac.be/

Software tool that predicts motifs in full-size peak sets. It performs all steps from motif discovery to visualization of the predicted sites in genome browsers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RSAT peak-motifs (RRID:SCR_010886) Copy   

•   Source: SciCrunch Registry

http://cisreg.cmmt.ubc.ca/TFFM/doc/

Software for Transcription Factor Flexible Models (TFFMs) that represent Transcription Factor Binding Sites (TFBSs) and are based on hidden Markov models (HMM). They are flexible and are able to model both position interdependence within TFBSs and variable length motifs within a single dedicated framework.

Proper citation: TFFM (RRID:SCR_010888) Copy   

•   Source: SciCrunch Registry

http://www.cs.ucr.edu/~polishka/

A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6

Proper citation: NOrMAL (RRID:SCR_010889) Copy   

•   Source: SciCrunch Registry

http://www.stat.wisc.edu/~keles/Software/demo_Nucde.pdf

An R package mapping nucleosome-linker boundaries from both MNase-Chip and MNase-Seq data using a non-homogeneous hidden-state model based on first order differences of experimental data along genomic coordinates.

Proper citation: NucDe (RRID:SCR_010893) Copy   

•   Source: SciCrunch Registry