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https://github.com/vals/umis

Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias.

Proper citation: umis (RRID:SCR_024381) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=survivalROC

Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data.

Proper citation: survivalROC (RRID:SCR_024415) Copy   

•   Source: SciCrunch Registry

https://github.com/ncbi/sra-tools/

Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces.

Proper citation: sra-toolkit (RRID:SCR_024350) Copy   

•   Source: SciCrunch Registry

https://github.com/MMV-Lab/mmv_im2im

Software Python package for image to image transformation in bioimaging applications. Can be used for semantic segmentation, instance segmentation, image restoration, image generation, and more.

Proper citation: MMV Im2Im (RRID:SCR_024630) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ggridges

Software R package enables creation of Ridgeline plots in 'ggplot2'

Proper citation: ggridges (RRID:SCR_024511) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gamm4

Software R package to estimate generalized additive mixed models.

Proper citation: gamm4 (RRID:SCR_024507) Copy   

•   Source: SciCrunch Registry

https://www.mathworks.com/products/optimization.html

Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations.

Proper citation: Optimization Toolbox (RRID:SCR_024486) Copy   

•   Source: SciCrunch Registry

https://github.com/danbider/lightning-pose

Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.

Proper citation: Lightning Pose (RRID:SCR_024480) Copy   

•   Source: SciCrunch Registry

https://github.com/navinlabcode/copykat

Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data.

Proper citation: CopyKAT (RRID:SCR_024512) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=classInt

Software R package for choosing univariate class intervals for mapping or other graphics purposes.

Proper citation: classInt (RRID:SCR_024515) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=mitml

Software R package for multiple imputation of missing data in multilevel modeling.

Proper citation: mitml (RRID:SCR_024516) Copy   

•   Source: SciCrunch Registry

http://www.grenoble.prabi.fr/obiwarehouse

OBIWarehouse (Open Biological Warehouse) aims at integrating several biological data sources into a unified database. Content includes 3D structural data, Protein-related data, Metabolic-related data, Genomic-related data, and Biological classification.

Proper citation: OBIWarehouse (RRID:SCR_010729) Copy   

•   Source: SciCrunch Registry

http://dictybase.org/teaching_tools/index.html

Dictyostelium discoideum is a great organism to use to teach cellular biology. It exhibits very interesting behaviors, such as chemotaxis and phagocytosis, that can readily be studied in standard laboratories without the need for expensive equipment. Lists of labs being used in real courses settings and all necessary information for performing those experiments are provided. Major headings: * Dictyostelium cell biology course, by Dr. David Knecht, University of Connecticut * Dictyostelium cell biology, by Dr. Derrick Brazill, Hunter College, New York * Report on the number of cells in a slug, contributed by John Bonner * Practical on chemotaxis, by Dr. Thierry Soldati, University of Geneva * Comments from Researchers * References suggested by contributors

Proper citation: dictyBase - Teaching Tools Using Dictyostelium discoideum (RRID:SCR_010701) Copy   

•   Source: SciCrunch Registry

http://toolkit.tuebingen.mpg.de/hhpred

The primary aim in developing HHpred was to provide biologists with a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred''s sensitivity is competitive with the most powerful servers for structure prediction currently available. HHpred is the first server that is based on the pairwise comparison of profile hidden Markov models (HMMs). Whereas most conventional sequence search methods search sequence databases such as UniProt or the NR, HHpred searches alignment databases, like Pfam or SMART. This greatly simplifies the list of hits to a number of sequence families instead of a clutter of single sequences. All major publicly available profile and alignment databases are available through HHpred.

Proper citation: HHpred (RRID:SCR_010276) Copy   

•   Source: SciCrunch Registry

http://bti.cornell.edu/

BTI is unique in being a private, not-for-profit research institute dedicated to plant biology, and located on a major university campus. Its mission is to advance and communicate scientific knowledge in plant biology to improve agriculture, protect the environment, and enhance human health. The institute was founded in Yonkers, New York, next to the home of its benefactor, William Boyce Thompson. In the mid-1970''s, however, it was recognized that a physical presence on a university campus would catapult the institute to a higher level of research, and the Cornell affiliation was born. BTI hires its own faculty, postdoctoral scholars and technicians, but also hosts undergraduate and graduate researchers from Cornell. BTI faculty generally have adjunct appointments at Cornell, and participate in graduate training and other university affairs. As envisioned in the Agreement of Affiliation, the partnership is advantageous for both parties, and contributes to a singularly strong environment for fundamental plant research on the campus. William Boyce Thompson founded BTI in 1924 on the premise that basic plant research leads to real benefits for people. Many potential applications of BTI research are to improve crops by increasing yield or nutritional content, or decreasing the need for harmful fertilizers and pesticides. Other research could lead to inexpensive plant-made vaccines, or even shed light on the human immune system. With aims like these in mind, scientists at BTI study life at the scale of genes and proteins to learn about processes such as how plants detect light, or how they respond when aphids bite into them. Along with research, BTI''s mission includes environmental responsibility and outreach to teachers, students, and community members. Though it remains an independent, non-profit institution, BTI is affiliated with Cornell University and is located on its Ithaca, New York campus.

Proper citation: Boyce Thompson Institute for Plant Research (RRID:SCR_010716) Copy   

•   Source: SciCrunch Registry

http://www.cise.ufl.edu/~abarmpou/lab/fanDTasia/

A Java applet tool for DT-MRI processing. It opens Diffusion-Weighted MRI datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser.

Proper citation: fanDTasia Java Applet: DT-MRI Processing (RRID:SCR_009624) Copy   

•   Source: SciCrunch Registry

http://downsyndrome.ucsd.edu/index.php

The Down Syndrome Center for Research and Treatment (DSCRT) is one of the first programs in the country to connect academic research with treatment of adults and children with Down syndrome. Our goal is to apply cutting edge basic research to develop treatments that will help people with Down syndrome improve their cognition and forestall the onset of Alzheimer''s disease. Members of this special population continue to live fuller, healthier lives. We hope to build on this progress and advance their potential even further. About 400,000 people with Down syndrome live in the U.S. today, and one in every 733 babies is born with the condition. Children with Down syndrome are at risk for congenital heart defects, respiratory and hearing problems, childhood leukemia, and thyroid conditions. They typically also have mild to moderate cognitive impairment that affects learning, memory and speech. This is an important topic for research. With increased health care, education, and societal support, people with Down syndrome are living longer, fuller lives. But as they age we are discovering an increased occurrence of the symptoms associated with Alzheimer''s disease. In fact, about 25 percent of individuals with Down syndrome over age 35 increasingly show clinical signs and symptoms of Alzheimer''s type dementia. By age 60, more than half show cognitive decline.

Proper citation: Down Syndrome Center for Research and Treatment (RRID:SCR_010627) Copy   

•   Source: SciCrunch Registry

http://www.horizonpress.com/gateway/

Molecular Biology Gateway is the gateway to Web resources for molecular biology, genomics, PCR, protocols, microbiology, and biochemistry. Major categories include: Current Molecular Biology News, Microbiology, Virology, Genomics and Bioinformatics, PCR, Journals, Books, and other Publications, Protocols, Technology, Books, and Recommended Reading.

Proper citation: Molecular Biology Gateway (RRID:SCR_010628) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-18/search?q=*&l=

A virtual database cataloging numerous data set resources, including: BrainMaps.org, Cell Centered Database, Clinical Trials Network (CTN) Data Share, ClinicalTrials.gov, CRCNS, Gene Expression Omnibus, ArrayExpress, MPD - Mouse Phenome Database, BioSharing, Gene Weaver, XNAT Central, 1000 Functional Connectomes Project, Health.Data.gov, SciCrunch Registry, NIF Registry Automated Crawl Data, NeuroVault, OpenfMRI, Physiobank, RanchoBiosciences, YPED, Data.gov Science, and Research Data Catalog.

Proper citation: Integrated Datasets (RRID:SCR_010503) Copy   

•   Source: SciCrunch Registry

http://annmap.picr.man.ac.uk/

A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser.

Proper citation: Annmap (RRID:SCR_011783) Copy   

•   Source: SciCrunch Registry