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http://transcriptome.ens.fr/eoulsan/

A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.

Proper citation: Eoulsan (RRID:SCR_011901) Copy   

•   Source: SciCrunch Registry

http://www.litinspector.org/

A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.

Proper citation: LitInspector (RRID:SCR_011870) Copy   

•   Source: SciCrunch Registry

http://vina.scripps.edu/

An open-source program for doing molecular docking.

Proper citation: AutoDock Vina (RRID:SCR_011958) Copy   

•   Source: SciCrunch Registry

http://scalpel.sourceforge.net/

A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).

Proper citation: Scalpel (RRID:SCR_012107) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/snpratiotest/

Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.

Proper citation: SNP ratio test (RRID:SCR_012070) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/compomics-utilities/

A software library containing code shared by many research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. This library can be of use to other research groups doing computational proteomics.

Proper citation: compomics-utilities (RRID:SCR_012073) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/pride-converter-2/

Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra.

Proper citation: PRIDE Converter 2 (RRID:SCR_012051) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/open-ms/

An algorithm to align LC-MS samples and to match corresponding ion species across samples.

Proper citation: OpenMS (RRID:SCR_012042) Copy   

•   Source: SciCrunch Registry

http://obi-warp.sourceforge.net/

Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.

Proper citation: OBI-Warp (RRID:SCR_012041) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/icplquant/

A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments.

Proper citation: ICPL ESIQuant (RRID:SCR_012047) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.11/bioc/html/easyRNASeq.html

Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.

Proper citation: easyRNASeq (RRID:SCR_012020) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mtoolbox/

Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.

Proper citation: MToolBox (RRID:SCR_012112) Copy   

•   Source: SciCrunch Registry

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

A user-friendly software tool to estimate allele-specific gene expression.

Proper citation: Allim (RRID:SCR_012114) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nailsystemsbiology/

A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.

Proper citation: NAIL (RRID:SCR_012134) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cohcap/

An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

Proper citation: COHCAP (RRID:SCR_006499) Copy   

•   Source: SciCrunch Registry

http://sammeth.net/confluence/display/FLUX/Home

Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver.

Proper citation: FLUX CAPACITOR (RRID:SCR_006651) Copy   

•   Source: SciCrunch Registry

http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/

An information-rich viewer for next-generation genome assembles with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation. EagleView is a multi-platform application developed with C++ and is available for all three major platforms: Windows, Linux, and Mac OS.

Proper citation: EagleView (RRID:SCR_006859) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bigpre/

A quality assessment software package for next-genomics sequencing data.

Proper citation: BIGpre (RRID:SCR_006781) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.12/bioc/html/seqbias.html

Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

Proper citation: seqbias (RRID:SCR_006832) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Software to detect rare or de novo copy number alterations in normal DNA samples. Please note that QuantiSNP is no longer under active development.

Proper citation: QuantiSNP (RRID:SCR_013091) Copy   

•   Source: SciCrunch Registry