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https://github.com/STOmics/StereoCell_v2.0
Enhanced application on generating single cell gene expression profile for high resolution spatial transcriptomics. Registers spatial gene expression map and cell membrane/wall staining image with nuclei staining image as intermediary, thus cell membrane/wall outlines can be directly segmented from cell membrane/wall staining image without correcting nuclei boundaries.
Proper citation: StereoCell v2.0 (RRID:SCR_024438) Copy
https://github.com/kblin/ncbi-acc-download
Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.
Proper citation: NCBI accession download script (RRID:SCR_024130) Copy
Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses.
Proper citation: Lucy (RRID:SCR_024099) Copy
Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA.
Proper citation: tacg (RRID:SCR_024374) Copy
Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide.
Proper citation: WHONET (RRID:SCR_024495) Copy
https://github.com/tseemann/VelvetOptimiser/
Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile.
Proper citation: VelvetOptimiser (RRID:SCR_024376) Copy
https://github.com/EGA-archive/ega-download-client
Software Python tool for viewing and downloading files from authorized European Genome-phenome Archive datasets. Python based EGA download client.
Proper citation: PyEGA (RRID:SCR_024654) Copy
Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations.
Proper citation: VisIt (RRID:SCR_024370) Copy
https://desmid.github.io/mview/
Web-compatible database search or multiple alignment viewer, Software tool as command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats.
Proper citation: MView (RRID:SCR_024129) Copy
AI based software for detecting integrity issues in figures of scientific articles. Used for detecting integrity issues in life science articles. Detects inappropriate manipulation and duplication in many figure types, including blots, microscopy images, and light photography.
Proper citation: ImageTwin (RRID:SCR_024543) Copy
http://www.juntadeandalucia.es/fundacionprogresoysalud/es/home
An organization that supports the public health system in Andalusia, Spain through three main activities: research and innovation in health, technologies line information and communication, and training and evaluation of professional skills. It also provides management support to the Health Quality Agency of Andalusia, which is the driving entity of the Andalusian Quality Model. Resource is in Spanish.
Proper citation: Progress and Health Foundation; Seville; Spain (RRID:SCR_000276) Copy
https://imagej.net/plugins/3d-imagej-suite/
Software suite provides plugins to enhance 3D capabilities of ImageJ.
Proper citation: 3D ImageJ Suite (RRID:SCR_024534) Copy
http://www.sanger.ac.uk/science/tools/ssaha2-0
A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.
Proper citation: Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) Copy
FAIR API ecosystem for inter-connected biomedical knowledge. Provides three components in its API development ecosystem: family of high-performance APIs for accessing up-to-date annotations for genes, genetic variants, chemicals and drugs; provides BioThings API packages its API-development best practice into reusable Software Development Kit to help other bioinformaticians to build same high-quality API to distribute their own specific knowledge; BioThings API provides platform to foster findability and interoperability across community developed biomedical APIs. Provides tools for authoring API metadata following community supported OpenAPI standard and hosts standardized interactive API documentation. Defines set of OpenAPI extensions to provide biomedical specific semantic annotations.
Proper citation: BioThings API (RRID:SCR_024539) Copy
http://rambok.sourceforge.net/
Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data.
Proper citation: rambo-k (RRID:SCR_024198) Copy
https://web.archive.org/web/20180316202959/http://zombie.cb.k.u-tokyo.ac.jp/sprai/
Software tool to correct sequencing errors in single pass reads for de novo assembly.
Proper citation: sprai (RRID:SCR_024353) Copy
https://intel.github.io/scikit-learn-intelex/latest/
Software tool as Intel(R) Extension for Scikit-learn to speed up Scikit-learn application. Used to accelerate existing scikit-learn code. Accelerates Scikit-learn applications and still have full conformance with all Scikit-Learn APIs and algorithms. Software AI accelerator brings over 10-100X acceleration across variety of applications.
Proper citation: scikit-learn-intelex (RRID:SCR_024595) Copy
https://github.com/streamlit/streamlit
Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps.
Proper citation: streamlit (RRID:SCR_024354) Copy
https://cme.h-its.org/exelixis/web/software/sweed/
Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.
Proper citation: sweed (RRID:SCR_024357) Copy
https://metacpan.org/dist/Bio-Tools-Run-Alignment-TCoffee
Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program.
Proper citation: Bio-Tools-Run-Alignment-TCoffee (RRID:SCR_024070) Copy
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