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http://www.cambridgecognition.com/

Global commercial provider of cognitive assessment software for clinical trials, academic research and healthcare provision.

Proper citation: Cambridge Cognition (RRID:SCR_003001) Copy   

•   Source: SciCrunch Registry

https://github.com/CRG-Barcelona/bwtool/wiki

A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted.

Proper citation: bwtool (RRID:SCR_003035) Copy   

•   Source: SciCrunch Registry

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

Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing.

Proper citation: enviPat (RRID:SCR_003034) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/gel2de/

Software application for performing pixel-by-pixel correlation analysis on a set of gel images from two-dimensional gel electrophoresis and a set of clinical parameters for a population. The application is written in C++, and has been tested on Windows, although it in principle should compile cross platform using CMake.

Proper citation: Gel2DE (RRID:SCR_002977) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/

Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided

Proper citation: ChIPMonk (RRID:SCR_002975) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View

An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results.

Proper citation: SMRT View (RRID:SCR_003029) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/pbh5tools

Software tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from cmp.h5 and bas.h5 files.

Proper citation: pbh5tools (RRID:SCR_003027) Copy   

•   Source: SciCrunch Registry

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

A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation.

Proper citation: ProRata (RRID:SCR_002988) Copy   

•   Source: SciCrunch Registry

https://www.fitzgerald-fii.com

Commercial organization that supplies antibodies, proteins, ELISA kits, serum, and plasma to the research community.

Proper citation: Fitzgerald Industries International (RRID:SCR_003237) Copy   

•   Source: SciCrunch Registry

https://www.assays.co.il

Commercial organization that provides services for assay development, research histopathology, and early stage project consultation.

Proper citation: Smart Assays (RRID:SCR_003195) Copy   

•   Source: SciCrunch Registry

http://www.stereologyresourcecenter.com/

A company of professionally trained stereologists, bioscientists, computer engineers, educators, and support personnel that provides comprehensive neurostereology products and services to the global bioscience community. These products and services include: stereology and image analysis software, digital imaging technology, turnkey stereologer solutions, comprehensive stereology and image analysis/image processing software, professional contract services, neurostereology workshops, basic stereology courses, and online stereology webinars. The Center also offers tissue processing (sectioning, staining, slide preparation) and stereology data collection services. Researchers may use equipment and facilities to complete projects with full confidentiality and according to Good Laboratory Practices guidelines.

Proper citation: Stereology Resource Center (RRID:SCR_003137) Copy   

•   Source: SciCrunch Registry

http://www.uccs.edu/

Public university that offers degrees in the social sciences, humanities, and natural sciences.

Proper citation: University of Colorado; Colorado Springs; USA (RRID:SCR_003130) Copy   

•   Source: SciCrunch Registry

http://mrsfast.sourceforge.net/

A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)

Proper citation: mrsFAST (RRID:SCR_003128) Copy   

•   Source: SciCrunch Registry

http://acgt.cs.tau.ac.il/hyden/

Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).

Proper citation: HYDEN (RRID:SCR_003126) Copy   

•   Source: SciCrunch Registry

http://www.hyperphagia.org/

Request for Applications to fund the best ideas in the field of hyperphagia research. Institutions of Higher Education, Nonprofit organizations, For-profit companies are eligible.

Proper citation: Hyperphagia (RRID:SCR_003157) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/orfer/

An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.

Proper citation: ORFprimer (RRID:SCR_003269) Copy   

•   Source: SciCrunch Registry

http://researchmaps.org/

UCLA based service for research planning aimed to help users integrate and summarize large amounts of information into a searchable graphic format. The interactive features facilitates planning during writing of grants, research papers and reviews. ResearchMaps can also be used as a collaborative tool and as a catalyst for the creative process.

Proper citation: ResearchMaps (RRID:SCR_003178) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gemi/

Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences.

Proper citation: Gemi (RRID:SCR_003211) Copy   

•   Source: SciCrunch Registry

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

Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Proper citation: QDNAseq (RRID:SCR_003174) Copy   

•   Source: SciCrunch Registry

http://www.popgen.dk/software/index.php/NgsAdmix

A tool for finding admixture proportions from next generation sequencing (NGS) data that is based on genotype likelihoods. It is a multithreaded c/c++ program.

Proper citation: NGSadmix (RRID:SCR_003208) Copy   

•   Source: SciCrunch Registry