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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems.
Proper citation: BD FACS Sortware sorter software (RRID:SCR_016722) Copy
Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap.
Proper citation: VectorMap (RRID:SCR_016721) Copy
http://www.nbtltd.com/products/smi-begaze%E2%84%A2-analysis-software
Software package for eye tracking studies by New Bio Technology Ltd. Used for designing eye movement studies and recording, analyzing, visualizing data of eye tracking results.
Proper citation: SMI BeGaze (RRID:SCR_016648) Copy
http://projects.biotec.tu-dresden.de/metapocket/
Software tool to identify pockets on protein surface to predict ligand-binding sites.
Proper citation: metaPocket (RRID:SCR_016653) Copy
Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes.
Proper citation: fermi (RRID:SCR_016652) Copy
Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data.
Proper citation: circular statistics (RRID:SCR_016651) Copy
Software tool for multi level analysis of applications optimized for ImageXpress instruments. High-content image analysis software featuring time lapse analysis. Used for 2D and 3D imaging.
Proper citation: MetaXpress (RRID:SCR_016654) Copy
Platform as a web-based interactive environment to automatically identify, explore and visualize homology and functional annotations for assembled transcripts.
Proper citation: Genotate (RRID:SCR_016659) Copy
https://github.com/WilsonSayresLab/XYalign
Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data.
Proper citation: XYalign (RRID:SCR_016661) Copy
Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Official Python library (API) used to create, read, and manipulate .loom files, supporting out-of-memory operations to handle datasets larger than RAM.
Proper citation: LoomPy (RRID:SCR_016666) Copy
http://www.ccb.jhu.edu/software/centrifuge/
Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers.
Proper citation: Centrifuge Classifier (RRID:SCR_016665) Copy
https://www.schrodinger.com/macromodel
Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex.
Proper citation: MacroModel (RRID:SCR_016747) Copy
Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information.
Proper citation: PaVE (RRID:SCR_016599) Copy
https://github.com/vaklip/transfer_learning_ccnn
Software program to implement transfer learning for a connectome convolutional neural network trained to classify functional connectomes using Tensorflow.
Proper citation: transfer_ learning_ ccnn (RRID:SCR_016590) Copy
https://tbportals.niaid.nih.gov
Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data.
Proper citation: TB PORTALS (RRID:SCR_016594) Copy
Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.
Proper citation: NMRProcFlow (RRID:SCR_016592) Copy
https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html
Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.
Proper citation: BLASTClust (RRID:SCR_016641) Copy
http://ecogenomics.github.io/CheckM/
Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes.
Proper citation: CheckM (RRID:SCR_016646) Copy
https://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi
Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus.
Proper citation: Genotyping (RRID:SCR_016645) Copy
https://www.ncbi.nlm.nih.gov/orffinder
Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long.
Proper citation: Open Reading Frame Finder (RRID:SCR_016643) Copy
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