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http://www.cbcb.umd.edu/software/metapath
A statistical package for comparing metagenomic data-sets at the pathway level. It relies on a combination of metagenomic sequence data and prior metabolic pathway knowledge, which is pulled from KEGG.
Proper citation: Metapath (RRID:SCR_014621) Copy
http://server.molgenrug.nl/index.php/prokaryote-promoters
A webserver for the prediction of prokaryote promoter elements and regulons. DNA in FASTA or plain format serve as input. A gene table can be included with the run.
Proper citation: PePPER Prokaryote Promoter Prediction (RRID:SCR_014740) Copy
http://huttenhower.sph.harvard.edu/humann
A pipeline which takes short DNA/RNA reads as inputs and produces gene and pathway summaries as outputs. The pipeline converts sequence reads into coverage and abundance tables summarizing the gene families and pathways in one or more microbial communities.
Proper citation: HUMAnN (RRID:SCR_014620) Copy
Matlab statistics toolbox allowing the computation of a wide range of measures of effect size. Four main toolbox functions cover common analysis designs, including two-sample-, oneway- and twoway- data sets as well as categorical data. Data may be repeated-measures.
Proper citation: Measures of Effect Size Toolbox (RRID:SCR_014703) Copy
Software used to simulate tumor progression in various stages of growth in order to study the process' dynamics. The input can be fitness landscape, mutation rate, and cell division time. The output is growth dynamics and other relevant statistics, such as expected tumor detection time and expected appearance time of surviving mutants. The tool is implemented in Java and runs on all operating systems which run a Java Virtual Machine (JVM) of version 1.7 or above.
Proper citation: Tool for Tumor Progression (RRID:SCR_014700) Copy
Computing platform for biomolecular NMR available to not-for-profit or government users. It consists of a virtual machine (VM) provisioned with dozens of widely-used NMR software packages, and is available as a cloud-based Platform-as-a-Service (PaaS) or as a downloadable VM for local execution.
Proper citation: NMRbox (RRID:SCR_014827) Copy
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/hclust.html
R documentation for hierarchical cluster analysis on a set of dissimilarities for n objects. Each object is assigned to its own cluster, which an algorithm proceeds through iteratively. Two of the most similar clusters are joined at each stage until there is a single cluster. Distances between clusters are recomputed at each stage by the Lance–Williams dissimilarity update formula according to the particular clustering method being used. Clustering methods include: Ward's minimum variance method, complete linkage method, and single linkage method.
Proper citation: Hierarchical Clustering (RRID:SCR_014673) Copy
https://github.com/jakejh/zeitzeiger
R package for regularized supervised learning on high-dimensional data from an oscillatory system. Zeitzeiger can quantify rhythmic behavior, make accurate predictions, identify major patterns and important features, and detect when the oscillator is perturbed.
Proper citation: Zeitzeiger (RRID:SCR_014791) Copy
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/prcomp.html
R documentation for a function that performs a principal components analysis on a given data matrix and returns the results as an object of class prcomp.
Proper citation: Principal Components Analysis (RRID:SCR_014676) Copy
Mobile software application for behavioral social science experiments on an online platform. It can be used on computers, tablets, and smartphones. It is hardware independent, does not require online connectivity to perform a test, and has the option of interfacing with outside sensors, such as heart rate or weighting scales.
Proper citation: Xperiment (RRID:SCR_014712) Copy
https://imdevsoftware.wordpress.com/software/
A software suite for data wrangling, creating interactive data visualization, performing statistical analyses, cluster analyses, exploratory data analysis and visualization (such as principal component analysis), predictive modeling and biochemical pathway analysis.
Proper citation: DeviumWeb (RRID:SCR_014683) Copy
https://github.com/cmayer/BaitFisher-package
Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.
Proper citation: Baitfisher (RRID:SCR_015985) Copy
Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Proper citation: Avogadro (RRID:SCR_015983) Copy
http://www.sanger.ac.uk/science/tools/seqtools
Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments.
Proper citation: Belvu (RRID:SCR_015989) Copy
https://github.com/sanger-pathogens/Bio-Tradis
Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.
Proper citation: Bio-tradis (RRID:SCR_015993) Copy
Web server implemented in JAVA and PHP for annotating genetic variants by m6A function. It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm. It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations.
Proper citation: m6ASNP: Annotation of genetic variants by m6A function (RRID:SCR_016048) Copy
Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: IMAGEN (RRID:SCR_016045) Copy
http://www.vicbioinformatics.com/software.barrnap.shtml
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Barrnap (RRID:SCR_015995) Copy
http://itolab.med.kyushu-u.ac.jp/BMap/index.html
Software that maps whole-genome and targeted bisulfite sequence reads to reference genomes. It is especially useful for reads obtained using post-bisulfite adaptor tagging (PBAT)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BMap (RRID:SCR_016044) Copy
https://www.nitrc.org/projects/normalizefov
FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets.
Proper citation: NeuroImage Field-of-View Normalization Tool (RRID:SCR_015957) Copy
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