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http://cran.r-project.org/web/packages/evora/

R package for quantifying variation in DNA methylation as a cancer biomarker.

Proper citation: EVORA (RRID:SCR_007329) Copy   

•   Source: SciCrunch Registry
  

http://seurat.r-forge.r-project.org/

Software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data. Visual analytics for the integrated analysis of microarray data.

Proper citation: SEURAT (RRID:SCR_007322) Copy   

•   Source: SciCrunch Registry
  

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

Bioinformatics analysis software tool for optimized ChIP-seq peak detection written in R.

Proper citation: peakrots (RRID:SCR_007453) Copy   

•   Source: SciCrunch Registry
  

https://github.com/steinmann/peakzilla

An algorithm to identify transcription factor binding sites from ChIP-seq data.

Proper citation: Peakzilla (RRID:SCR_007471) Copy   

•   Source: SciCrunch Registry
  

http://www.imperial.ac.uk/AP/faces/pages/read/Home.jsp?person=l.coin&_adf.ctrl-state=pekvgdj4t_3&_afrRedirect=4092914325174000

Software for identifying haplogroups from low coverage sequence data.

Proper citation: YHap (RRID:SCR_007951) Copy   

•   Source: SciCrunch Registry
  

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

A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.

Proper citation: AmpliconNoise (RRID:SCR_007814) Copy   

•   Source: SciCrunch Registry
  

http://web1.sph.emory.edu/users/hwu30/polyaPeak.html

An R package for ranking ChIP-seq peaks with shape information.

Proper citation: polyaPeak (RRID:SCR_007687) Copy   

•   Source: SciCrunch Registry
  

http://www.ensembl.org/info/docs/tools/vep/index.html

Data analysis service to predict the functional consequences of known and unknown variants.

Proper citation: Variant Effect Predictor (RRID:SCR_007931) Copy   

•   Source: SciCrunch Registry
  

http://www.annoj.org/

A REST-based web application designed for visualizing deep sequencing data and other genome annotation data.

Proper citation: Anno-J (RRID:SCR_008192) Copy   

•   Source: SciCrunch Registry
  

https://sites.google.com/site/dadadenoiser/

Infers both the sample genotypes and error parameters that produced a metagenome data set.

Proper citation: DADA (RRID:SCR_008205) Copy   

•   Source: SciCrunch Registry
  

https://github.com/eturro/mmseq#mmseq-transcript-and-gene-level-expression-analysis-using-multi-mapping-rna-seq-reads

Software package that contains a collection of statistical tools for analysing RNA-seq expression data.

Proper citation: MMSEQ (RRID:SCR_008184) Copy   

•   Source: SciCrunch Registry
  

http://cbil.upenn.edu/BEERS/

A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl.

Proper citation: BEERS (RRID:SCR_005090) Copy   

•   Source: SciCrunch Registry
  

http://flux.sammeth.net/capacitor.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Software that aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing.

Proper citation: Flux Simulator (RRID:SCR_005088) Copy   

•   Source: SciCrunch Registry
  

http://minia.genouest.org/

A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.

Proper citation: Minia (RRID:SCR_004986) Copy   

•   Source: SciCrunch Registry
  

http://compbio.cs.huji.ac.il/NucPosition/TemplateFiltering/Home.html

A software pipeline for analyzing deep sequencing maps of chromatin structure.

Proper citation: TemplateFilter (RRID:SCR_004980) Copy   

•   Source: SciCrunch Registry
  

http://drive5.com/uparse/

An Operational Taxonomic Unit (OTU) clustering software for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures.

Proper citation: UPARSE (RRID:SCR_005020) Copy   

•   Source: SciCrunch Registry
  

http://www.cebitec.uni-bielefeld.de/index.php/2-uncategorised/47-carma?highlight=WyJjYXJtYSJd

A software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system.

Proper citation: CARMA (RRID:SCR_004999) Copy   

•   Source: SciCrunch Registry
  

http://smd.princeton.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser.

Proper citation: SMD (RRID:SCR_004987) Copy   

•   Source: SciCrunch Registry
  

http://mitcr.milaboratory.com/

An open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data. It is designed with the knowledge of the critical challenges arising in everyday processing of immunological data.

Proper citation: MiTCR (RRID:SCR_004989) Copy   

•   Source: SciCrunch Registry
  

http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/

A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer.

Proper citation: MIP Scaffolder (RRID:SCR_005072) Copy   

•   Source: SciCrunch Registry