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http://www.nxstage.com/

A medical device company that develops, manufactures and markets innovative dialysis systems for the treatment of end-stage renal disease, or ESRD, and acute kidney failure.

Proper citation: NxStage Medical (RRID:SCR_004000) Copy   

•   Source: SciCrunch Registry
  

http://purl.bioontology.org/ontology/MPATH

A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes

Proper citation: Mouse Pathology Ontology (RRID:SCR_003950) Copy   

•   Source: SciCrunch Registry
  

http://purl.bioontology.org/ontology/NHSQI2009

Ontology to organise a 2009 set of over 200 NHS quality indicators from different sources. Relationships between indicators, a basic set of inclusion / exclusion criteria, clinical pathway, clinical code and purpose (per 1992 Institute of Medicine, originally intended to categorise clinical guidelines) are identifies and made searchable.

Proper citation: NHS Quality Indicators (RRID:SCR_004005) Copy   

•   Source: SciCrunch Registry
  

https://www.selectscience.net/suppliers/sirius-analytical/?compID=5860

Organization that designs and manufactures analytical instrumentation to measure physicochemical parameters for the pharmaceutical and biotech industry, as well as offers physicochemical data and consultancy services. Their instruments provide accurate and reliable values for pKa, log P, log D, solubility and dissolution, particle size and shape analysis. These critical physicochemical parameters are important in drug formulation, and also influence the ability of New Chemical Entities to cross biological membranes such as the gastro-intestinal tract, blood-brain barrier, skin and cell walls. Sirius also offers an analytical service for high quality PhysChem outsourcing, used by hundreds of clients worldwide.

Proper citation: Sirius Analytical (RRID:SCR_003945) Copy   

•   Source: SciCrunch Registry
  

https://www.corengi.com/

A comprehensive, free, and interactive platform to help individuals discover more about clinical trials that may be appropriate for them for a variety of diseases. The platform allows stakeholders within the clinical trials community (investigators, site personnel, sponsors, and disease advocates) to engage with potential enrollees and educate them about specific clinical trials. They have identified some of the most commonly used criteria for the clinical trials in each disease. Using these criteria, they developed a questionnaire for a single disease. Then, looking at just those questions, they can start to get a sense of which clinical trials might be appropriate for a particular person which is a helpful to start to narrow down the list of potentially appropriate trials. All clinical trials that are posted on www.clinicaltrials.gov for the diseases that Corengi covers will be on the website.

Proper citation: Corengi (RRID:SCR_003942) Copy   

•   Source: SciCrunch Registry
  

http://www.almirall.com/

A pharmaceutical company committed to provide valuable medicines through their own R&D efforts, licenses and collaborations. Through seeking innovative medicines they aim to become a relevant player in respiratory and dermatology diseases with also a strong interest in gastroenterology and pain. The company is headquartered in Barcelona, Spain, and has 14 affiliates in Europe and North America and trading capacity in 22 countries.

Proper citation: Almirall (RRID:SCR_003947) Copy   

•   Source: SciCrunch Registry
  

http://skylign.org/

A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position.

Proper citation: Skylign (RRID:SCR_001176) Copy   

•   Source: SciCrunch Registry
  

https://rdrr.io/bioc/sRAP/

Software package that provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.

Proper citation: sRAP (RRID:SCR_001297) Copy   

•   Source: SciCrunch Registry
  

https://rdrr.io/bioc/yaqcaffy/

Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

Proper citation: yaqcaffy (RRID:SCR_001295) Copy   

•   Source: SciCrunch Registry
  

http://122.228.158.106/BSSim/

Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD.

Proper citation: BSSim (RRID:SCR_001212) Copy   

•   Source: SciCrunch Registry
  

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

Software package that uses a modeling strategy especially designed for normalizing high-throughput genomic data. The premise is that your data is a function of study-specific variables which are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.

Proper citation: SNM (RRID:SCR_001299) Copy   

•   Source: SciCrunch Registry
  

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

Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

Proper citation: ChIPsim (RRID:SCR_001293) Copy   

•   Source: SciCrunch Registry
  

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data.

Proper citation: methyAnalysis (RRID:SCR_001290) Copy   

•   Source: SciCrunch Registry
  

http://julian-gehring.github.io/les/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.

Proper citation: les (RRID:SCR_001291) Copy   

•   Source: SciCrunch Registry
  

http://ccb.jhu.edu/software/sim4cc/

Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.

Proper citation: sim4cc (RRID:SCR_001204) Copy   

•   Source: SciCrunch Registry
  

http://qualimap.bioinfo.cipf.es/

Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.

Proper citation: QualiMap (RRID:SCR_001209) Copy   

•   Source: SciCrunch Registry
  

http://www.omixon.com/data-analysis-and-pro/

Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets.

Proper citation: Omixon Target Data Analysis (RRID:SCR_001207) Copy   

•   Source: SciCrunch Registry
  

https://www.bioconductor.org/packages//2.10/bioc/html/beadarraySNP.html

Software package for importing data from Illumina SNP experiments and performing copy number calculations and reports.

Proper citation: beadarraySNP (RRID:SCR_001281) Copy   

•   Source: SciCrunch Registry
  

http://josephryan.github.io/baa.pl/

Software tool to evaluate de novo genome assemblies with RNA transcripts.

Proper citation: Baa.pl (RRID:SCR_001197) Copy   

•   Source: SciCrunch Registry
  

http://pathology.wustl.edu/VirusHunter/

A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses.

Proper citation: VirusHunter (RRID:SCR_001198) Copy   

•   Source: SciCrunch Registry