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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://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://savannah.gnu.org/projects/datamash/

Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts.

Proper citation: Datamash (RRID:SCR_016067) 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

http://aspiredb.msl.ubc.ca/

Web based software for analyzing genomic variants CNVs, SNVs, and Indels and phenotypes. It aims to represent the relationships between discovered variants and phenotypes.

Proper citation: AspireDB (RRID:SCR_016272) 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://www.jamovi.org/

Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience.

Proper citation: jamovi (RRID:SCR_016142) Copy   

•   Source: SciCrunch Registry

https://www.picoquant.com/products/category/software

Software for fluorescence lifetime imaging and correlation. SymPhoTime 64 is the data acquisition software for PicoQuant's time-resolved confocal microscope MicroTime 200 and LSM upgrade kits.

Proper citation: SymPhoTime 64 (RRID:SCR_016263) Copy   

•   Source: SciCrunch Registry

http://www.birds.cornell.edu/brp/raven/RavenOverview.html

Software for the acquisition, visualization, measurement, and analysis of sounds. Raven supports annotations for research-related analysis.

Proper citation: Raven (RRID:SCR_016190) Copy   

•   Source: SciCrunch Registry

http://www.heka.com/downloads/downloads_main.html#down_fitmaster

Software for analysis and fitting routines of electrophysiological data. Analysis can be performed on the levels of Sweeps/Traces and Series.

Proper citation: FITMASTER (RRID:SCR_016233) Copy   

•   Source: SciCrunch Registry

http://www.redshirtimaging.com/redshirt_neuro/software_aquisition.htm

Software for acquisition and analysis for imaging applications. The acquisition section has a variety of triggering and averaging modes, while the analysis section has extensive provisions for displaying traces (intensity vs time) and movies of propagating activity.

Proper citation: NeuroPlex (RRID:SCR_016193) 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://cole-trapnell-lab.github.io/monocle-release/docs/

Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.

Proper citation: Monocle2 (RRID:SCR_016339) Copy   

•   Source: SciCrunch Registry

https://github.com/KM-Lab/Electrographic-Seizure-Analyzer

Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.

Proper citation: Electrographic Seizure Analyzer (RRID:SCR_016344) Copy   

•   Source: SciCrunch Registry

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

Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Proper citation: MAST (RRID:SCR_016340) 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://easyfmri.github.io

Software that employs machine learning techniques and high-performance computing for analyzing task-based fMRI datasets. It applies Feature Analysis, Hyperalignment, Multi-voxel Pattern Analysis (MVPA), Representational Similarity Analysis (RSA), and more.

Proper citation: Easy fMRI (RRID:SCR_016392) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pubmed/23489480

Software package for image analysis to determine the orientation of filamentous structures on digital images. Used as an image‐processing tool for analyzing cytoskeleton and cellulose fiber orientation in pant imagesk.

Proper citation: MicroFilament Analyzer (RRID:SCR_016411) Copy   

•   Source: SciCrunch Registry

https://omictools.com/splicing-express-tool

Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems.

Proper citation: Splicing Express (RRID:SCR_016498) Copy   

•   Source: SciCrunch Registry