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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://biothings.io/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/magnusmanske/snpomatic

Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping,

Proper citation: snpomatic (RRID:SCR_024348) Copy   

•   Source: SciCrunch Registry

https://www.certara.com/software/phoenix-pkpd/

Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool.

Proper citation: WinNonlin (RRID:SCR_024504) Copy   

•   Source: SciCrunch Registry

https://github.com/harvardinformatics/NGmerge

Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates.

Proper citation: NGmerge (RRID:SCR_024483) Copy   

•   Source: SciCrunch Registry

http://www.workrave.org/

Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage.

Proper citation: Workrave (RRID:SCR_024364) Copy   

•   Source: SciCrunch Registry

http://xmedcon.sourceforge.net/

Open source software toolkit for medical image conversion.

Proper citation: XMedCon (RRID:SCR_024366) Copy   

•   Source: SciCrunch Registry

http://www.ks.uiuc.edu/Research/vmd/

Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Proper citation: VMD (RRID:SCR_024368) Copy   

•   Source: SciCrunch Registry

https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/dna-amplicon.html

Local Run Manager DNA Amplicon analysis module aligns amplicon reads against reference specified in the manifest file. Variants are called for the targeted regions.

Proper citation: DNA Amplicon (RRID:SCR_024481) Copy   

•   Source: SciCrunch Registry

https://github.com/miRTop/mirtop

Command lines tool to annotate miRNAs with standard mirna/isomir naming.

Proper citation: mirtop (RRID:SCR_024116) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/mpsqed/

Software tool for the design of multiplex pyrosequencing assays.

Proper citation: mPSQed (RRID:SCR_024118) Copy   

•   Source: SciCrunch Registry

http://www-igm.univ-mlv.fr/~marsan/smile_english.html

Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.

Proper citation: SMILE (RRID:SCR_024119) Copy   

•   Source: SciCrunch Registry