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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/package=parmigene
Software R package for parallel estimation of mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for reconstruction of gene regulatory networks.
Proper citation: parmigene (RRID:SCR_024285) Copy
https://cran.r-project.org/web/packages/pcaPP/index.html
Software R package provides functions for principal component analysis by projection pursuit.
Proper citation: pcapp (RRID:SCR_024287) Copy
https://cran.r-project.org/package=psychotree
Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models.
Proper citation: psychotree (RRID:SCR_024288) Copy
http://saint-apms.sourceforge.net/Main.html
Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.
Proper citation: saint (RRID:SCR_024324) Copy
https://cran.r-project.org/web/packages/dynamicTreeCut/index.html
Software R package contains methods for detection of clusters in hierarchical clustering dendrograms.
Proper citation: dynamicTreeCut (RRID:SCR_024280) Copy
https://github.com/artic-network/readucks
Software package as Nanopore read de-multiplexer.
Proper citation: readucks (RRID:SCR_024315) Copy
https://cran.r-project.org/package=stringi
Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing.
Proper citation: stringi (RRID:SCR_024319) Copy
Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments.
Proper citation: VARNA (RRID:SCR_024373) Copy
https://github.com/vgteam/vg#vg
Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes.
Proper citation: variation graph (RRID:SCR_024369) Copy
https://sourceforge.net/projects/trinculo/
Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping.
Proper citation: Trinculo (RRID:SCR_024384) Copy
https://cran.r-project.org/package=Rwave
Software R package provides environment for Time-Frequency analysis of 1-D signals.
Proper citation: rwave (RRID:SCR_024302) Copy
Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias.
Proper citation: umis (RRID:SCR_024381) Copy
https://github.com/ncbi/sra-tools/
Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces.
Proper citation: sra-toolkit (RRID:SCR_024350) Copy
http://bioinformatics.psb.ugent.be/orcae/
Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community.
Proper citation: Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) Copy
Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support.
Proper citation: libRoadRunner (RRID:SCR_014763) Copy
https://rostlab.org/owiki/index.php/PROFisis
Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures.
Proper citation: PROFisis (RRID:SCR_024179) Copy
http://contra.stanford.edu/contrafold/
Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.
Proper citation: CONTRAfold (RRID:SCR_023994) Copy
https://github.com/bioinfo-center-pasteur-fr/toppred
Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.
Proper citation: toppred (RRID:SCR_024385) Copy
https://rostlab.org/owiki/index.php/Metastudent
Software tool to predict gene ontology terms for protein sequences through homology.
Proper citation: Metastudent (RRID:SCR_024110) Copy
https://github.com/bartongroup/yanosim
Software tool as read simulator for nanopore DRS datasets.
Proper citation: Yanosim (RRID:SCR_024363) Copy
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