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

Software package that detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples.

Proper citation: MMDiff (RRID:SCR_012692) Copy   

•   Source: SciCrunch Registry
  

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

Software package that identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines.

Proper citation: baySeq (RRID:SCR_012795) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/excavatortool/

A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data.

Proper citation: EXCAVATOR-tool (RRID:SCR_012766) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/devel/bioc/html/RPA.html

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.

Proper citation: RPA (RRID:SCR_012768) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sequencing

Whole genome secondary analysis on Illumina sequencing platforms.

Proper citation: Isaac (RRID:SCR_012772) Copy   

•   Source: SciCrunch Registry
  

https://github.com/torognes/swipe

A software tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases.

Proper citation: SWIPE (RRID:SCR_012771) Copy   

•   Source: SciCrunch Registry
  

http://sift.bii.a-star.edu.sg/

Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.

Proper citation: SIFT (RRID:SCR_012813) Copy   

•   Source: SciCrunch Registry
  

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

Software that provides an integrated solution for the Illumina microarray data analysis.

Proper citation: lumi (RRID:SCR_012781) Copy   

•   Source: SciCrunch Registry
  

http://bioinf.comav.upv.es/ngs_backbone/index.html

A bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences.

Proper citation: Ngs backbone (RRID:SCR_012907) Copy   

•   Source: SciCrunch Registry
  

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

This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data.

Proper citation: rqubic (RRID:SCR_012869) Copy   

•   Source: SciCrunch Registry
  

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

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Proper citation: DiffBind (RRID:SCR_012918) Copy   

•   Source: SciCrunch Registry
  

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

A bi-clustering algorithm which is optimizes for binary data analysis.

Proper citation: iBBiG (RRID:SCR_012882) Copy   

•   Source: SciCrunch Registry
  

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.bioconductor.org/packages/2.12/bioc/html/TurboNorm.html

Software providing a fast scatterplot smoother suitable for microarray normalization based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.

Proper citation: TurboNorm (RRID:SCR_012963) 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://sourceforge.net/projects/mirdeepstar/

An integrated application software tool for miRNA identification from RNA sequencing data.

Proper citation: miRDeep* (RRID:SCR_012960) Copy   

•   Source: SciCrunch Registry
  

http://www.geneprof.org/GeneProf/

A database of curated, integrated and reusable high-throughput genomics experiments and a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; Next-Generation Sequencing or NGS). Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf. Existing software can be easily wrapped and integrated in the GeneProf framework and data from GeneProf may be used externally.

Proper citation: GeneProf (RRID:SCR_012927) 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