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http://www.bioconductor.org/packages/release/bioc/html/eisa.html

A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data.

Proper citation: eisa (RRID:SCR_012883) Copy   

•   Source: SciCrunch Registry

http://www.fda.gov/

An agency of the United States Department of Health and Human Services, one of the United States federal executive departments that is responsible for protecting and promoting public health through the regulation and supervision of food safety, tobacco products, dietary supplements, prescription and over-the-counter pharmaceutical drugs (medications), vaccines, biopharmaceuticals, blood transfusions, medical devices, electromagnetic radiation emitting devices (ERED), cosmetics and veterinary products. The FDA also enforces other laws, notably Section 361 of the Public Health Service Act and associated regulations, many of which are not directly related to food or drugs. These include sanitation requirements on interstate travel and control of disease on products ranging from certain household pets to sperm donation for assisted reproduction. (Wikipedia)

Proper citation: U.S. Food and Drug Administration (RRID:SCR_012945) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/methylumi.html

Software package that provides classes for holding and manipulating Illumina methylation data.

Proper citation: Methylumi (RRID:SCR_012831) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/iChip.html

Software package that uses hidden Ising models to identify enriched genomic regions in ChIP-chip data.

Proper citation: iChip (RRID:SCR_012958) Copy   

•   Source: SciCrunch Registry

http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/drompa/

A software program for peak-calling and visualization for ChIP-seq analysis.

Proper citation: DROMPA (RRID:SCR_012928) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/NarrowPeaks.html

Software package for post-processing of peaks and differential binding in ChIP-seq based on standard wiggle visualization files. The double aim of the package is to apply a functional version of principal component analysis (FPCA) to: (1) Process data in wiggle track format (WIG) commonly produced by ChIP-seq peak finders by applying FPCA over a set of selected candidate enriched regions. This is done in order to shorten the genomic locations accounting for a given proportion of variation among the enrichment-score profiles. The function ''narrowpeaks'' allows the user to discriminate between binding regions in close proximity to each other and to narrow down the length of the putative transcription factor binding sites while preserving the information present in the variability of the dataset and capturing major sources of variation. (2) Analyze differential variation when multiple ChIP-seq samples need to compared. The function ''narrowpeaksDiff'' quantifies differences between the tag-enrichment, and uses non-parametric tests on the FPC scores for testing differences between conditions.

Proper citation: NarrowPeaks (RRID:SCR_012924) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/ChAMP.html

Software package that includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.

Proper citation: ChAMP (RRID:SCR_012891) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/trowel-ec/

An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.

Proper citation: Trowel (RRID:SCR_012890) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/CSAR.html

Statistical tools for the analysis of ChIP-seq data.

Proper citation: CSAR (RRID:SCR_012930) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/CSSP.html

Software for power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.

Proper citation: CSSP (RRID:SCR_012932) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/cghMCR.html

Software package that provides functions to identify genomic regions of interest based on segmented copy number data from multiple samples.

Proper citation: cghMCR (RRID:SCR_012898) Copy   

•   Source: SciCrunch Registry

http://www.dei.unipd.it/~sambofra/abacus.html

An Algorithm based on a BivAriate CUmulative Statistic to identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions.

Proper citation: ABACUS (RRID:SCR_013039) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/oncosts/

Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments.

Proper citation: Onco-STS (RRID:SCR_012990) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/RankProd.html

Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp).

Proper citation: RankProd (RRID:SCR_013046) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nxgview/

A virtual software pipeline that contains several PERL modules for processing next generation sequencing data.

Proper citation: NxGview (RRID:SCR_012994) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bamformatics/

Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.

Proper citation: Bamformatics (RRID:SCR_013041) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/MEDIPS.html

Software developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq).

Proper citation: MEDIPS (RRID:SCR_012996) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bsmapper/

Sequence mapper for bisulfite sequencing reads for DNA methylation studies.

Proper citation: BSmapper (RRID:SCR_012998) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mendelscan/

A software tool for prioritizing candidate variants in family-based studies of inherited disease.

Proper citation: MendelScan (RRID:SCR_013053) Copy   

•   Source: SciCrunch Registry

http://mathgen.stats.ox.ac.uk/impute/impute_v2.html

A computer program for phasing observed genotypes and imputing missing genotypes.

Proper citation: IMPUTE2 (RRID:SCR_013055) Copy   

•   Source: SciCrunch Registry