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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.
https://cran.r-project.org/web/packages/NMF/index.html
Software R package provides framework to perform Non-negative Matrix Factorization.Used for nonnegative matrix factorization.Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.
Proper citation: nmf (RRID:SCR_024284) Copy
https://cran.r-project.org/package=pROC
Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Proper citation: proc (RRID:SCR_024286) Copy
https://cran.r-project.org/package=psyphy
Software R package useful in analyzing data from psychophysical experiments.Includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice data to be used with binomial family in glm and self-Start functions for estimating gamma values for CRT screen calibrations.
Proper citation: psyphy (RRID:SCR_024289) Copy
Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.
Proper citation: ruby-bio (RRID:SCR_024322) Copy
https://github.com/ggonnella/rgfa
Ruby library for handling GFA files.
Proper citation: rgfa (RRID:SCR_024323) Copy
https://cran.r-project.org/web/packages/OptimalCutpoints/index.html
Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures.
Proper citation: optimalcutpoints (RRID:SCR_024283) Copy
https://cran.r-project.org/web/packages/rpact/index.html
Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints.
Proper citation: rpact (RRID:SCR_024300) Copy
https://cran.r-project.org/web/packages/shazam/index.html
Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis.
Proper citation: shazam (RRID:SCR_024301) Copy
https://github.com/rrwick/Unicycler
Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline.
Proper citation: Unicycler (RRID:SCR_024380) Copy
https://github.com/dib-lab/sourmash
Software library for MinHash sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets.
Proper citation: sourmash (RRID:SCR_024347) Copy
http://tab2mage.sourceforge.net/
Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database.
Proper citation: tab2mage (RRID:SCR_024359) Copy
http://www-personal.umich.edu/~jianghui/rseq/
A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.
Proper citation: rSeq (RRID:SCR_000562) Copy
https://services.healthtech.dtu.dk/services/DictyOGlyc-1.1/
Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
Proper citation: DictyOGlyc (RRID:SCR_001600) Copy
http://www.glycosciences.de/modeling/glyprot/
Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php
Proper citation: GlyProt (RRID:SCR_001560) Copy
Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database.
Proper citation: Phospho.ELM (RRID:SCR_001109) Copy
http://hipipe.ncgm.sinica.edu.tw/
Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task.
Proper citation: HiPipe (RRID:SCR_001215) Copy
Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers.
Proper citation: ImJoy (RRID:SCR_020935) Copy
http://srna-workbench.cmp.uea.ac.uk
Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals.
Proper citation: UEA sRNA Workbench (RRID:SCR_020947) Copy
https://github.com/telatin/covtobed
Software tool to generate BED coverage tracks from BAM files.
Proper citation: covtobed (RRID:SCR_023998) Copy
http://bioinfo.unl.edu/gramalign.php
Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences.
Proper citation: GramAlign (RRID:SCR_024032) Copy
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