Tools   Select Another Resource Report Type

http://code.google.com/p/frhit/

An efficient fragment recruitment software program for next generation sequences against microbial reference genomes. It produces similar sensitivity of BLASTN, but runs at a 100 times higher speed. The algorithm adopts a seeding heuristic strategy with overlapping k-mer hashing to locate candidate matching blocks on the reference sequences, and then apply an effective filtering within the candidate blocks to filter out blocks that do not meet the minimum criteria for containing an alignment with specified parameters. For each candidate block that passed the filter, the best matching sub-regions between a candidate block and a read are determined, and used subsequently by the banded Smith-Waterman algorithm to carry out the actual alignment efficiently, which will finally verify if this can be a valid recruitment hit.

Proper citation: FR-HIT (RRID:SCR_002181) Copy   

•   Source: SciCrunch Registry

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

Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments.

Proper citation: metaRNASeq (RRID:SCR_002174) Copy   

•   Source: SciCrunch Registry

http://www.genoscope.cns.fr/spip/spip.php?lang=en

French national sequencing center with the following resources: * Sequencing ** Genoscope Projects * Environmental genomics ** Microbial diversity in wastewater ** Metabolic genomics * Bioinformatics ** Atelier for comparative genomics ** Computational Systems Biology ** Servers resources *** GGB for Generic Genome Browser: graphic interface for various databases (sequence, annotation, syntenies...) for a given organism. *** MaGe for Magnifying Microbial Genomes: annotation system for microbial genomes.

Proper citation: Genoscope (RRID:SCR_002172) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/demi/

R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes.

Proper citation: DEMI (RRID:SCR_002291) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions.

Proper citation: flowCore (RRID:SCR_002205) Copy   

•   Source: SciCrunch Registry

http://wiki.biac.duke.edu/jvs:cigal

Software program that provides accurate real-time stimulus control, behavioral and physiological recording, and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings (e.g. screen color) and a list of stimulus events, which can include images, animated movies, sound files, text stimuli, video graphics, or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL's real-time programming capabilities. Output files can be automatically created in a variety of output formats (e.g. FSL 3-column files, XML Events files, CSV trial tables).

Proper citation: CIGAL (RRID:SCR_002232) Copy   

•   Source: SciCrunch Registry

http://cbi.nyu.edu/software/niftimatlab.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28, 2025. Software tool that allows the user to operate on NIfTI image files from Matlab.

Proper citation: NIfTImatlab (RRID:SCR_002230) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/uncbcp_4d_atlas/

Software package for constructing longitudinal atlases, which are the necessary steps for many brain-related applications.

Proper citation: 4D Atlases Construction (RRID:SCR_002227) Copy   

•   Source: SciCrunch Registry

http://www.clsi.org/

A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world.

Proper citation: Clinical and Laboratory Standards Institute (RRID:SCR_002382) Copy   

•   Source: SciCrunch Registry

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

Scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease) intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic 1 hour session at 3T. Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format. Please cite: Bennett. A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. ?Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study?, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047

Proper citation: Multi-Modal MRI Reproducibility Resource (RRID:SCR_002442) Copy   

•   Source: SciCrunch Registry

http://cogprints.org/

An electronic archive for self-archive papers in any area of Psychology, neuroscience, and Linguistics, and many areas of Computer Science, Philosophy, Biology, Medicine, Anthropology, cognitive ethnology, archeology, paleontology, as well as any other portions of the physical, social and mathematical sciences that are pertinent to the study of cognition.

Proper citation: Cogprints: Cognitive Sciences EPrint Archive (RRID:SCR_002314) Copy   

•   Source: SciCrunch Registry

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

A software package to analyze flow cytometric data using gate information to follow population / community dynamics.

Proper citation: flowCyBar (RRID:SCR_002319) Copy   

•   Source: SciCrunch Registry

http://www.ncdc.noaa.gov/paleo/softlib/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. A simple, efficient, process-based forward model of tree-ring growth, requires as inputs only latitude and monthly temperature and precipitation.

Proper citation: VS-Lite (RRID:SCR_002431) Copy   

•   Source: SciCrunch Registry

http://www.ncdc.noaa.gov/paleo/softlib/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. Matlab code for two-factor (location and year) analysis-of-variance model for the calculation of climate anomalies, in which the reference interval is specified as the full length of the dataset. This scheme avoids the affects of shorter (e.g. 1961-1990) reference intervals on the temporal evolution of the spatial standard deviation of climate anomalies. Data files provided.

Proper citation: ANOVA (RRID:SCR_002427) Copy   

•   Source: SciCrunch Registry

https://github.com/nh13/DWGSIM

Whole Genome Simulator for Next-Generation Sequencing.

Proper citation: DWGSIM (RRID:SCR_002342) Copy   

•   Source: SciCrunch Registry

http://www.arizona.edu/

Public research university in Tucson, Arizona that offers undergraduate and graduate degree programs in psychology, audiology, speech pathology, and medicine.

Proper citation: University of Arizona; Arizona; USA (RRID:SCR_002459) Copy   

•   Source: SciCrunch Registry

https://github.com/PhKoch/RepARK

Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome.

Proper citation: RepARK (RRID:SCR_002333) Copy   

•   Source: SciCrunch Registry

http://atsbio.com/

Commercial supplier of antibodies, assay kits, conjugates and various toxins for biomedical research. ATS's product line is designed to assist scientists in the study of system functions, cell functionality, diseases and disorders.

Proper citation: Advanced Targeting Systems (RRID:SCR_002328) Copy   

•   Source: SciCrunch Registry

http://neuronetrix.com/

A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker).

Proper citation: COGNISION (RRID:SCR_002362) Copy   

•   Source: SciCrunch Registry

http://www07.grants.gov/applicants/find_grant_opportunities.jsp

A source to FIND and APPLY for federal grants. The U.S. Department of Health and Human Services is proud to be the managing partner for Grants.gov, an initiative that is having an unparalleled impact on the grant community. All discretionary grants offered by the 26 federal grant-making agencies can be found on Grants.gov. Grants.gov was established as a governmental resource named the E-Grants Initiative, part of the President's 2002 Fiscal Year Management Agenda to improve government services to the public. The concept has its origins in the Federal Financial Assistance Management Improvement Act of 1999, also known as Public Law 106-107. Public Law 106-107 has since sunset and is now known as the Grants Policy Committee (GPC). For more information on the Grants Policy Committee, click here. Today, Grants.gov is a central storehouse for information on over 1,000 grant programs and provides access to approximately $500 billion in annual awards. You may find information on *What is a Grant? *Who is Eligible for a Grant? *Program highlights and accomplishments *Grants.gov in the News (Articles, press releases, milestones and events) *Program Status (Detailed information about our relationship with partner federal agencies, financial contributions, grant opportunities, fiscal reports, planning strategies and statistics.)

Proper citation: Grants.gov (RRID:SCR_002661) Copy   

•   Source: SciCrunch Registry