SciCrunch

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.

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SciCrunch
10 years ago - submitted by Kristen Jensen

BMTagger

A tool that discriminates between human reads and microbial reads without performing an alignment of all reads to the human genome.

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SciCrunch
10 years ago - submitted by Kristen Jensen

SitePainter

An interactive data visualization tool which allows users to create and upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Fast-Unifrac

THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. Provides a suite of tools for the comparison of microbial communities using phylogenetic information.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Unifrac

THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample.

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SciCrunch
10 years ago - submitted by Kristen Jensen

speciateIT

A software package for speciation of 16S sequence data.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Simrank

A rapid and sensitive general-purpose k-mer search tool.

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SciCrunch
10 years ago - submitted by Kristen Jensen

HMPTrees

An R-package which uses Object Oriented Data Analysis (OODA) methods to analyze taxonomic trees directly, providing tools to model, compare, and visualize populations of taxonomic tree objects.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

An R-package which uses Dirichlet-Multinomial distribution to perform formal hypothesis testing on the species abundance distribution of human microbiome data, and to calculate power and sample size requirements for human microbiome experiments.

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SciCrunch
10 years ago - submitted by Kristen Jensen

MicrobiomeUtilities

A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Metastats

A statistical software package for comparing metagenomic datasets and clinical data sets comprised of two treatment populations, with each treatment population being made up of multiple samples. It relies on a non-parametric t-test.

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SciCrunch
10 years ago - submitted by Kristen Jensen

LEfSe

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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SciCrunch
10 years ago - submitted by Kristen Jensen

inVUE

An API and software suite for large scale data visualization and analysis.

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SciCrunch
10 years ago - submitted by Kristen Jensen

GINGKO

A GUI software package to help non-expert statisticians conduct multivariate analysis methods. Various multivariate analysis methods are available, including correspondance analysis, aglomerative hierarchical clustering, related multidimensional scaling, and discriminant analysis (linear, quadratic or distance-based).

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SciCrunch
10 years ago - submitted by Kristen Jensen

RAST Server

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

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SciCrunch
10 years ago - submitted by Kristen Jensen

IMG System

Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Core Gene Evaluation Script

A tool used to screen for core gene sets as an indicator of completeness of draft genomes. The download includes a Perl script and required archaeal and bacterial core genes fasta and cluster files.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Pathogen Portal

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. A set of web-based resources provided by the Bioinformatics Resource Centers (BRCs), focusing on organisms considered as potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. It provides data sets of host responses to pathogens and genome data, as well as tools to analyze host responses to pathogens.

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SciCrunch
10 years ago - submitted by Ko-Wei Lin

FactoMineR

Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.

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RRID-Legacy
10 years ago - by Anonymous

ggplot2

Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.

Resource
RRID-Legacy
10 years ago - by Anonymous

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