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https://bioconductor.org/packages/ReactomePA/
Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.
Proper citation: ReactomePA (RRID:SCR_019316) Copy
https://github.com/BNadel/GEDIT
Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices.
Proper citation: GEDIT (RRID:SCR_019277) 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
Open source software suite for mass spectrometry based proteomics. Software repository and collection of free software for analysis of mass spectrometry data. Software and code snippets for visualization and analysis of mass spectrometry data with emphasis on automated methods for proteomics and protein analysis.
Proper citation: ms-utils.org (RRID:SCR_019810) Copy
https://github.com/statOmics/tradeSeq
Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data.
Proper citation: tradeSeq (RRID:SCR_019238) 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://bioconductor.org/packages/release/bioc/html/PhenStat.html
Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.
Proper citation: PhenStat (RRID:SCR_021317) Copy
http://topaz.gatech.edu/GeneMark/
Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark.
Proper citation: GeneMarkS-T (RRID:SCR_017648) Copy
Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.
Proper citation: Mousebytes (RRID:SCR_017904) Copy
https://github.com/TomSexton00/4See
Software tool to visualize 4C data.
Proper citation: 4See (RRID:SCR_018014) 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/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
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/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
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
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
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
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