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https://github.com/BauerLab/ngsane

Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data.

Proper citation: NGSANE (RRID:SCR_003478) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/snape-pooled/

Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.

Proper citation: SNAPE-pooled (RRID:SCR_003476) Copy   

•   Source: SciCrunch Registry

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

Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.

Proper citation: Bpipe (RRID:SCR_003471) Copy   

•   Source: SciCrunch Registry

http://www.lgm.upmc.fr/parseq/

Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders.

Proper citation: Parseq (RRID:SCR_003464) Copy   

•   Source: SciCrunch Registry

http://ims.cochrane.org/revman/about-revman-5

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically.

Proper citation: RevMan (RRID:SCR_003581) Copy   

•   Source: SciCrunch Registry

http://www.chemokine.com/

An Antibody supplier

Proper citation: Torrey Pines Biolabs (RRID:SCR_003580) Copy   

•   Source: SciCrunch Registry

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

Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

Proper citation: MultiPhen (RRID:SCR_003498) Copy   

•   Source: SciCrunch Registry

http://www.biostat.wisc.edu/~kendzior/EBSEQ/

Software R package for RNA-Seq Differential Expression Analysis.

Proper citation: EBSeq (RRID:SCR_003526) Copy   

•   Source: SciCrunch Registry

http://www.hsph.harvard.edu/skat/metaskat/

A R package for multiple marker meta-analysis.

Proper citation: MetaSKAT (RRID:SCR_003489) Copy   

•   Source: SciCrunch Registry

http://genomesavant.com/p/home/index

A next-generation genome browser software designed for the latest generation of genome data.

Proper citation: Savant (RRID:SCR_003488) Copy   

•   Source: SciCrunch Registry

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

A Java interface to the mzTab data exchange format for reporting a summary of proteomics results.

Proper citation: jmzTab (RRID:SCR_003481) Copy   

•   Source: SciCrunch Registry

http://neweng.cau.ac.kr/

Private comprehensive research university in South Korea. Starting as a church-run kindergarten in 1918, CAU transformed into a school for female kindergarten teachers in 1922 and was granted university status in 1953.

Proper citation: Chung-Ang University; Seoul; South Korea (RRID:SCR_003547) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/mpg/magenta/

A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input.

Proper citation: MAGENTA (RRID:SCR_003422) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/RAREMETAL

A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.

Proper citation: RAREMETAL (RRID:SCR_003573) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ccsegthickness

An end-to-end pipeline for corpus callosum processing that provides automated midsagittal alignment, CC segmentation with a quality control tool, and thickness profile generation. Groupwise analysis is facilitated by permutation testing with FWER and FDR multiple comparison correction. Results display is facilitated by a display script that shows p-values on a 3D pipe representation of a CC. This pipeline is implemented in MATLAB and requires the Image Processing Toolbox. There are plans to implement it completely in Python.

Proper citation: Corpus Callosum Thickness Profile Analysis Pipeline (RRID:SCR_003575) Copy   

•   Source: SciCrunch Registry

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

A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms.

Proper citation: FadE (RRID:SCR_003448) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/proteomecommons-tranche/

A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most.

Proper citation: Proteome Commons Tranche repository (RRID:SCR_003441) Copy   

•   Source: SciCrunch Registry

http://www.compgen.org/tools/metagen

Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.

Proper citation: metagen (RRID:SCR_003443) Copy   

•   Source: SciCrunch Registry

http://www-pmr.ch.cam.ac.uk/wiki/Oscar3

OSCAR is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries. This tool for shallow, chemistry-specific parsing of chemical documents identifies (or attempts to identify): * Chemical names: singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names. * Ontology terms: if you can do it by string-matching, you can get OSCAR to do it. * Chemical data: Spectra, melting/boiling point, yield etc. in experimental sections. In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing (OPSIN), and with identifiers from the chemical ontology ChEBI Current work on OSCAR3 by Peter Corbett focuses on its use in SciBorg, a framework for the deep parsing of chemical text. OSCAR3 also includes the Oscar Server, a Jetty-powered set of servlets. These provide the following services: * Parsing of text/HTML by OSCAR. * Text/InChI/SMILES/SMILES substructues/SMILES similarity search of papers, coupled with keyword and ontology-based search, using Lucene and the CDK. * List of all names found / all names that co-occur with a search term or terms. * Online management of a chemical/stopword lexicon. * Manual editing of SciXML fragments containing named entities, for creating of gold standards and training data. Oscar3 can be found on SourceForge: http://sourceforge.net/projects/oscar3-chem/

Proper citation: Oscar3 (RRID:SCR_004561) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS/

Sequence orthology based software for improved taxonomic estimation of metagenomic sequences.

Proper citation: SOrt-ITEMS (RRID:SCR_004716) Copy   

•   Source: SciCrunch Registry