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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 Computer Assisted Medical Intervention Tool Kit helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.Open source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations.
Proper citation: CamiTK (RRID:SCR_023984) Copy
https://github.com/aberer/RogueNaRok
Software tool as versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index.
Proper citation: roguenarok (RRID:SCR_024316) Copy
http://faculty.washington.edu/tathornt/software/ROADTRIPS2/
Software C program that performs single SNP, case control association testing in samples with partially or completely unknown population and pedigree structure.
Proper citation: roadtrips (RRID:SCR_024318) Copy
https://github.com/brentp/vcfanno
Software tool for flexible annotation of genetic variants.Extracts and summarizes attributes from multiple annotation files and integrates annotations within INFO column of the original VCF file.
Proper citation: vcfanno (RRID:SCR_024372) Copy
https://github.com/walaj/SeqLib
Software C++ htslib/bwa-mem/fermi interface for interrogating sequence data
Proper citation: SeqLib (RRID:SCR_024091) Copy
https://bitbucket.org/genomicepidemiology/virulencefinder
Software tool for detection of E. coli virulence genes. Used to identify viruelnce genes in total or partial sequenced isolates of bacteria. E. coli, Enterococcus, S. aureus and Listeria are available.for detection of E. coli virulence genes.
Proper citation: VirulenceFinder (RRID:SCR_024371) Copy
http://johnhommer.com/academic/code/aghermann
Sotware tool designed to run Process S simulations on Slow Wave Activity profiles from human EEG recordings.Produces set of sleep homeostat parameters which can be used to describe and differentiate individual sleepers, such as short vs long sleepers, early vs late, etc.Sleep research experiment manager, with facility for reading, displaying, and manual and semi-automatic scoring EEG recordings in edf format; conventional PSD and EEG Microcontinuity profiles; artifact detection; Independent Component Analysis; basic sleep analysis NREM-REM cycle detection.
Proper citation: Aghermann (RRID:SCR_023965) Copy
http://www.bioinformatics.org/strap/
Software tool as Intuitive Editor for annotated multiple Sequence and Structure Alignments.
Proper citation: strap-base (RRID:SCR_024351) Copy
https://github.com/nanoporetech/qcat
Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
Proper citation: qcat (RRID:SCR_024195) Copy
https://github.com/gem-pasteur/macsyfinder
Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
Proper citation: MacSyFinder (RRID:SCR_024106) Copy
https://github.com/SciLifeLab/TIDDIT
Software tool as structural variant calling.
Proper citation: tiddit (RRID:SCR_024361) Copy
https://github.com/Adamtaranto/Yanagiba
Software tool to filter and slice Nanopore reads which have been basecalled with Albacore.
Proper citation: Yanagiba (RRID:SCR_024362) Copy
https://github.com/mateidavid/nanocall
Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller.
Proper citation: Nanocall (RRID:SCR_024124) Copy
https://github.com/torognes/swarm
Software tool as clustering method for amplicon-based studies.
Proper citation: swarm (RRID:SCR_024358) Copy
http://sourceforge.net/projects/phenofam/
A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.
Proper citation: PhenoFam (RRID:SCR_000640) Copy
http://faculty.washington.edu/browning/floss/floss.htm
Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software)
Proper citation: FLOSS (RRID:SCR_000836) Copy
http://www.sanger.ac.uk/science/tools/dindel
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems).
Proper citation: DINDEL (RRID:SCR_001827) Copy
http://animalgene.umn.edu/pedigraph/
A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles
Proper citation: PEDIGRAPH (RRID:SCR_001938) Copy
A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses.
Proper citation: Apollo (RRID:SCR_001936) Copy
Open source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime.
Proper citation: PsychoPy (RRID:SCR_006571) Copy
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