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http://www.nitrc.org/projects/gimme/

Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels.

Proper citation: GIMME (RRID:SCR_014115) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/pilon/

Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.

Proper citation: Pilon (RRID:SCR_014731) Copy   

•   Source: SciCrunch Registry

https://www.metaboanalyst.ca/

Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification.

Proper citation: MetaboAnalyst (RRID:SCR_015539) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/ariba

Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

Proper citation: Ariba (RRID:SCR_015976) Copy   

•   Source: SciCrunch Registry

http://kmer.sourceforge.net

Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.

Proper citation: Atac (RRID:SCR_015980) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/scater.html

Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.

Proper citation: scater (RRID:SCR_015954) Copy   

•   Source: SciCrunch Registry

https://CalRapp.org

A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates.

Proper citation: CalR (RRID:SCR_015849) Copy   

•   Source: SciCrunch Registry

https://www.biacore.com/lifesciences/service/downloads/software_licenses/biaevaluation/

Analysis software for life science data. This software package is for presentation and evaluation of sensorgram data from real-time BIA analyses.

Proper citation: BIAevaluation Software (RRID:SCR_015936) Copy   

•   Source: SciCrunch Registry

http://autodock.scripps.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock.

Proper citation: Autogrid (RRID:SCR_015982) Copy   

•   Source: SciCrunch Registry

https://github.com/kdmurray91/axe

Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples.

Proper citation: Axe (RRID:SCR_015984) Copy   

•   Source: SciCrunch Registry

https://github.com/pezmaster31/bamtools/wiki

Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.

Proper citation: Bamtools (RRID:SCR_015987) Copy   

•   Source: SciCrunch Registry

https://github.com/markmikkelsen/Gannet

Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data.

Proper citation: Gannet (RRID:SCR_016049) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/SimonHTausch/HiLive

Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications.

Proper citation: HiLive (RRID:SCR_016134) Copy   

•   Source: SciCrunch Registry

https://github.com/Ashod/garli

Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution.

Proper citation: GARLI (RRID:SCR_016117) Copy   

•   Source: SciCrunch Registry

https://github.com/bbuchfink/diamond

Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.

Proper citation: DIAMOND (RRID:SCR_016071) Copy   

•   Source: SciCrunch Registry

http://acb.qfab.org/acb/glam2/

Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.

Proper citation: Glam2 (RRID:SCR_016129) Copy   

•   Source: SciCrunch Registry

http://genometools.org

Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization.

Proper citation: GenomeTools (RRID:SCR_016120) Copy   

•   Source: SciCrunch Registry

https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGtfToGe_db software loads GTF files to a database for Genome Explorer. It allows the user to browse the results through the GE.

Proper citation: loadGtfToGe_db (RRID:SCR_015998) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/metagenomics/

Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.

Proper citation: MGnify (RRID:SCR_016429) Copy   

•   Source: SciCrunch Registry

https://gemma.msl.ubc.ca/phenotypes.html

Database that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. Part of Gemma, a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data.

Proper citation: Phenocarta (RRID:SCR_016273) Copy   

•   Source: SciCrunch Registry