Tools   Select Another Resource Report Type

https://metacpan.org/pod/Bio::CUA

Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems.

Proper citation: Codon Usage Analyzer (RRID:SCR_018500) Copy   

•   Source: SciCrunch Registry

https://github.com/xiaeryu/SpoTyping-v2.0

Software tool for fast and accurate in silico Mycobacterium spoligotyping from sequence reads.

Proper citation: SpoTyping (RRID:SCR_018466) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/timezone1/

Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes.

Proper citation: TimeZone (RRID:SCR_018564) Copy   

•   Source: SciCrunch Registry

https://github.com/blackrim/phyutility

Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI.

Proper citation: Phyutility (RRID:SCR_018545) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/pyflakes/

Software tool to check Python source files for errors. Passive checker of Python programs Used to analyze programs and detect various errors. Works by parsing source file, not importing it, so it is safe to use on modules with side effects.

Proper citation: Pyflakes (RRID:SCR_018422) Copy   

•   Source: SciCrunch Registry

https://github.com/yanzhanglab/Graph2GO

Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology.

Proper citation: Graph2GO (RRID:SCR_018726) Copy   

•   Source: SciCrunch Registry

https://imspectordocs.readthedocs.io/en/latest/intro.html

Software tool for real time analysis and data visualization. Software system for experimental control and quantitative data analysis in microscopy and spectroscopy.Integration of data processing and acquisition allows real time analysis and visualization of experimental results.

Proper citation: Imspector (RRID:SCR_018863) Copy   

•   Source: SciCrunch Registry

https://github.com/TMinchington/sass

Software tool as custom analysis code combining single-cell traces and spot detection from live imaging movies and using Imaris output.

Proper citation: Simple Assignment of Spots to Surfaces (RRID:SCR_018797) Copy   

•   Source: SciCrunch Registry

https://github.com/GGFHF/NGScloud2

Software tool for RNA-seq analysis of non model species using cloud computing. Provides user friendly front end to operate Amazon hardware resources and to control workflows of bioinformatic analysis of de novo RNA-seq, reference-based RNA-seq and functional annotation specifically oriented to plant species.

Proper citation: NGScloud2 (RRID:SCR_018716) Copy   

•   Source: SciCrunch Registry

https://github.com/chris-mcginnis-ucsf/DoubletFinder

Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data.

Proper citation: DoubletFinder (RRID:SCR_018771) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/scTHI/

Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.

Proper citation: scTHI (RRID:SCR_018918) Copy   

•   Source: SciCrunch Registry

https://github.com/najasplus/hetindel_shinyapp

Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.

Proper citation: Hetindel (RRID:SCR_018922) Copy   

•   Source: SciCrunch Registry

http://www.nonlinear.com/progenesis/qi-for-proteomics/

Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics.

Proper citation: Progenesis QI (RRID:SCR_018923) Copy   

•   Source: SciCrunch Registry

https://www.nccor.org/

Brings together Centers for Disease Control and Prevention, National Institutes of Health, Robert Wood Johnson Foundation, and U.S. Department of Agriculture to accelerate progress in reducing childhood obesity in America, to manage projects and reach common goals, to coordinate funding to make the most of available resources, to share insights and expertise to strengthen research. NCCOR focuses on efforts that have to benefit children, teens, and their families, and communities in which they live.

Proper citation: National Collaborative on Childhood Obesity Research (RRID:SCR_019150) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/vmas_2020/

Software tool to generate whole connected 3D brain ventricular shape model and encode ventricular surface deformation information that is inaccessible by ventricle volume measure. Contains automated segmentation approach and surface based multivariate morphometry statistics.

Proper citation: Ventricular Morphometry Analysis System (RRID:SCR_019007) Copy   

•   Source: SciCrunch Registry

https://github.com/medema-group/bigslice

Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data.

Proper citation: BiG-SLiCE (RRID:SCR_019130) Copy   

•   Source: SciCrunch Registry

https://biosimulators.org

Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects.

Proper citation: BioSimulators (RRID:SCR_019111) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/

Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.

Proper citation: PROCHECK (RRID:SCR_019043) Copy   

•   Source: SciCrunch Registry

https://github.com/bgcarlisle/TRNscreener

Software tool as R script to provide function that takes two arguments: path to folder of plain text files named by their DOI, and output filename. For each file in folder, it searches for trial identifiers based on regex matching and writes CSV that contains all trial registration numbers and in case of ClinicalTrials.gov entries, whether they correspond to registry entry on ClinicalTrials.gov.

Proper citation: Trial Registration Number screener (RRID:SCR_019211) Copy   

•   Source: SciCrunch Registry

http://www.biosoft.com/w/calcusyn.htm

Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools.

Proper citation: CalcuSyn (RRID:SCR_020251) Copy   

•   Source: SciCrunch Registry