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https://code.google.com/p/bsmap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A specifically designed version of BSMAP for reduced representation bisulfite sequencing (RRBS).

Proper citation: RRBSMAP (RRID:SCR_010864) Copy   

•   Source: SciCrunch Registry

http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS

An algorithm that allows researchers to identify transcript factor binding sites from paired-end sequencing reads. SIPeS uses a dynamic baseline directly through the piling up of fragments to effectively find peaks, overcoming the disadvantage of estimating the average length of DNA fragments from singled-end sequencing achieving more powerful prediction binding sites with high sensitivity and specificity.

Proper citation: SIPeS (RRID:SCR_010865) Copy   

•   Source: SciCrunch Registry

http://www.math.miami.edu/~vhower/tpic.html

A software for determining DNA/protein binding sites from a ChIP-Seq experiment.

Proper citation: T-PIC (RRID:SCR_010867) Copy   

•   Source: SciCrunch Registry

http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPDiff.htm

Provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2).

Proper citation: ChIPDiff Library Comparison (RRID:SCR_010871) Copy   

•   Source: SciCrunch Registry

http://biodoop-seal.sourceforge.net/

A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.

Proper citation: SEAL (RRID:SCR_010914) Copy   

•   Source: SciCrunch Registry

http://www.mhh.de/acghtool.html

A software tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs.

Proper citation: aCGHtool (RRID:SCR_010915) Copy   

•   Source: SciCrunch Registry

https://earray.chem.agilent.com/cghanalytics/index.html

A comprehensive design and analysis tool for setting up and interpreting your microarray experiments.

Proper citation: Agilent Genomic Workbench (RRID:SCR_010918) Copy   

•   Source: SciCrunch Registry

http://pages.cs.wisc.edu/~kliang/DBChIP/

Detects differential binding of transcription factors with ChIP-seq.

Proper citation: DBChIP (RRID:SCR_010872) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/DIME/index.html

R-package for identifying differential ChIP-seq based on an ensemble of mixture models.

Proper citation: DIME (RRID:SCR_010874) Copy   

•   Source: SciCrunch Registry

http://www.cs.ucf.edu/~xiaoman/ChIPModule/ChIPModule.html

A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data.

Proper citation: ChIPModule (RRID:SCR_010877) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst

A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

Proper citation: CloudBurst (RRID:SCR_010911) Copy   

•   Source: SciCrunch Registry

http://erne.sourceforge.net/

A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.

Proper citation: ERNE (RRID:SCR_010912) Copy   

•   Source: SciCrunch Registry

http://fureylab.web.unc.edu/software/fseq/

A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

Proper citation: F-Seq (RRID:SCR_010880) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer

An interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data.

Proper citation: ABySS-Explorer (RRID:SCR_010980) Copy   

•   Source: SciCrunch Registry

http://dnptrapper.sourceforge.net/

An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.

Proper citation: DNPTrapper (RRID:SCR_010981) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye

A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors.

Proper citation: Hawkeye (RRID:SCR_010982) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org

International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.

Proper citation: Mouse Genome Informatics (MGI) (RRID:SCR_006460) Copy   

•   Source: SciCrunch Registry

http://tardis.nibio.go.jp/homstrad/

A curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER. These structure-based alignments are annotated with JOY and examined individually.

Proper citation: HOMSTRAD - Homologous Structure Alignment Database (RRID:SCR_006544) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/geo/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.

Proper citation: NCBI Epigenomics (RRID:SCR_006151) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CCDS/

Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly.

Proper citation: Consensus CDS (RRID:SCR_006729) Copy   

•   Source: SciCrunch Registry