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http://centre.bioinformatics.zj.cn/mirtools/
A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome.
Proper citation: mirTools (RRID:SCR_009701) Copy
https://github.com/srp33/ShinyLearner
Software framework for performing benchmarks of machine learning classification algorithms. Containerized benchmarking tool for machine-learning classification of tabular data.
Proper citation: ShinyLearner (RRID:SCR_017608) Copy
https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT
Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.
Proper citation: NeuroChaT (RRID:SCR_018020) Copy
https://github.com/PapenfussLab/bionix
Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language.
Proper citation: BioNix (RRID:SCR_017662) Copy
https://github.com/hariszaf/pema
Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution.
Proper citation: PEMA (RRID:SCR_017676) Copy
https://github.com/theislab/anndata
Software tool that provides scalable way of keeping track of data and learned annotations. Initially built for Scanpy. Used as generic class for handling annotated data matrices. Stores data matrix with annotations of observations (samples, cells) and variables (features, genes), and unstructured annotations.
Proper citation: Anndata (RRID:SCR_018209) Copy
Web tool for display, annotation and management of phylogenetic trees. Accessible with any modern web browser.
Proper citation: iTOL (RRID:SCR_018174) Copy
http://mummer.sourceforge.net/
Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.
Proper citation: MUMmer (RRID:SCR_018171) Copy
https://github.com/molgor/biospytial
Software package as spatial graph based computing engine for ecological big data. Modular open source knowledge engine designed to import, organize, analyse and visualize big spatial ecological datasets using power of graph theory. Handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. Data are linked with relationships that are stored in graph database, while tabular and geospatial data are stored in relational database management system.
Proper citation: biospytial (RRID:SCR_018226) Copy
http://www.cbs.dtu.dk/services/NetMHCpan/
Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).
Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy
https://github.com/sysu-yanglab/TDimpute
Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data.
Proper citation: TDimpute (RRID:SCR_018306) Copy
https://github.com/hangyabalazs/opeth
Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them.
Proper citation: Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) Copy
Web server to predict ΔGapp for membrane insertion of potential TM helix. Given amino acid sequence of putative transmembrane helix, server gives prediction of corresponding apparent free energy difference for insertion of this sequence into Endoplasmic Reticulum membrane by means of Sec61 translocon.
Proper citation: ΔG prediction server (RRID:SCR_018191) Copy
https://github.com/galaxyproteomics/mvpapplication-git.git
Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach.
Proper citation: Multi-omics Visualization Platform (RRID:SCR_018077) Copy
http://dichroweb.cryst.bbk.ac.uk/html/home.shtml
Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures.
Proper citation: DichroWeb (RRID:SCR_018125) Copy
https://web.expasy.org/protparam/
Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.
Proper citation: ProtParam Tool (RRID:SCR_018087) Copy
https://www.machado.cnptia.embrapa.br/plantannot
Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard.
Proper citation: Plant Co-expression Annotation Resource (RRID:SCR_018429) Copy
http://emboss.bioinformatics.nl/cgi-bin/emboss/pepwheel
Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation.
Proper citation: pepwheel (RRID:SCR_018398) Copy
http://www.cbs.dtu.dk/services/MaxAlign/
Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area.
Proper citation: MaxAlign (RRID:SCR_018552) Copy
http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE
Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation.
Proper citation: GalaxyRefine (RRID:SCR_018531) Copy
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