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https://github.com/SionBayliss/PIRATE

Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds.

Proper citation: PIRATE (RRID:SCR_017265) Copy   

•   Source: SciCrunch Registry
  

https://github.com/hillerlab/GenomeAlignmentTools

Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences.

Proper citation: RepeatFiller (RRID:SCR_017414) Copy   

•   Source: SciCrunch Registry
  

http://www.itksnap.org/pmwiki/pmwiki.php

Software as open source, multiplatform tool used to segment structures in 3D medical images.

Proper citation: ITK-SNAP (RRID:SCR_017341) Copy   

•   Source: SciCrunch Registry
  

http://snf-515788.vm.okeanos.grnet.gr/

Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DIANA-mirPath (RRID:SCR_017354) Copy   

•   Source: SciCrunch Registry
  

http://trimal.cgenomics.org/

Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.

Proper citation: trimAl (RRID:SCR_017334) Copy   

•   Source: SciCrunch Registry
  

https://hnn.brown.edu/

Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data.

Proper citation: Human Neocortical Neurosolver (RRID:SCR_017437) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://github.com/YosefLab/FastProject

Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored.

Proper citation: FastProject (RRID:SCR_017462) Copy   

•   Source: SciCrunch Registry
  

https://amp.pharm.mssm.edu/geneshot/

Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.

Proper citation: Geneshot (RRID:SCR_017582) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Mangul-Lab-USC/telescope

Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted.

Proper citation: Telescope (RRID:SCR_017626) Copy   

•   Source: SciCrunch Registry
  

http://www.yasara.org/

Software tool to obtain structural guidance in biocatalytic investigations. Program for molecular visualising, modelling, and dynamics. Initial stage YASARA View is for free while higher stages YASARA Model, YASARA Dynamics, YASARA Structure require license fee. Program for Windows, Linux, MacOS and Android. YASARA View is available for free and contains all functions to explore macromolecular structure interactively.

Proper citation: YASARA (RRID:SCR_017591) Copy   

•   Source: SciCrunch Registry
  

https://amoebadb.org/amoeba/

Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers.

Proper citation: AmoebaDB (RRID:SCR_017592) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://bowtie-bio.sourceforge.net/crossbow/index.shtml

A scalable software pipeline for whole genome resequencing analysis.

Proper citation: Crossbow (RRID:SCR_013306) Copy   

•   Source: SciCrunch Registry
  

http://tomcatbackup.esat.kuleuven.be/inclusive/

A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

Proper citation: INCLUSive (RRID:SCR_013488) Copy   

•   Source: SciCrunch Registry
  

http://hannonlab.cshl.edu/Alta-Cyclic/main.html

An Illumina Genome-Analyzer (Solexa) base caller.

Proper citation: Alta-Cyclic (RRID:SCR_013373) Copy   

•   Source: SciCrunch Registry
  

http://www.osirix-viewer.com/

:OsiriX is an image processing software dedicated to DICOM images (.dcm / .DCM extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality (STORE SCP - Service Class Provider, STORE SCU - Service Class User, and Query/Retrieve) . OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT). The 3D Viewer offers all modern rendering modes: Multiplanar reconstruction (MPR), Surface Rendering, Volume Rendering and Maximum Intensity Projection (MIP). All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT). Osirix is at the same time a DICOM PACS workstation for medical imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. :

Proper citation: OsiriX Medical Imaging Software (RRID:SCR_013618) Copy   

•   Source: SciCrunch Registry
  

http://bioinformatics.ai.sri.com/ptools/

A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks.

Proper citation: Pathway Tools (RRID:SCR_013786) Copy   

•   Source: SciCrunch Registry
  

http://www.metabolomicsworkbench.org

Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops.

Proper citation: Metabolomics Workbench (RRID:SCR_013794) Copy   

•   Source: SciCrunch Registry